Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database

PubMed Central

Arita, Masanori; Suwa, Kazuhiro

2008-01-01

Background In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. Results To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available. Conclusion This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated. PMID:18822113

Elementary software for the hand lens identification of some common iranian woods

Treesearch

Vahidreza Safdari; Margaret S. Devall

2009-01-01

A computer program, “Hyrcania”, has been developed for identifying some common woods (26 hardwoods and 6 softwoods) from the Hyrcanian forest type of Iran. The program has been written in JavaScript and is usable with computers as well as mobile phones. The databases use anatomical characteristics (visible with a hand lens) and wood colour, and can be searched in...

Glove utilization in the prevention of cross transmission: a systematic review.

PubMed

Picheansanthian, Wilawan; Chotibang, Jutamas

2015-05-15

Gloves are worn to protect hands from contamination from microorganisms and to reduce the risks of transmission of microorganisms from healthcare workers to patients and vice versa. However, gloves should be changed between patient contacts and hand washing is necessary before putting on gloves and immediately after removing gloves. The objective of this review was to evaluate and synthesize the best available research evidence that investigates clinical use of gloves in the prevention of cross transmission. Health care workers.Types of intervention(s): Glove use intervention. Types of outcomes: Contamination of healthcare workers' hands, transmission of infections, adherence to glove usage, inappropriate uses of gloves, and adherence to hand hygiene. Types of studies: Quasi-experimental studies and descriptive studies. The search sought to find published and unpublished studies. The time period of the search covered articles published from 2000 to 2012 in English and Thai. The databases searched included: MEDLINE, CINAHL, EMBASE, The Cochrane Library, PubMed, Science Direct, Current Content Connect, Blackwell synergy, Thai Nursing Research Database, Thai thesis database, Digital Library of Thailand Research Fund, Research of National Research Council of Thailand, and Database of Office of Higher Education. Studies selected for retrieval were assessed by two independent reviewers for methodological quality using the Joanna Briggs Institute Meta-Analysis of Statistics Assessment and Review Instrument software. Data extraction was performed using the standardized data extraction tool from the Joanna Briggs Institute Meta-Analysis of Statistics Assessment and Review Instrument software. A meta-synthesis was not possible due to the methodological heterogeneity of the included papers. The evidence was thus presented as a narrative summary. Twenty-three studies were included in this review. The results indicated that contamination of a healthcare worker's gloves with bacteria during routine care activities is common. The use of gloves can protect the hands of healthcare workers from bacterial contamination, but the protection afforded by the gloves was incomplete. Adherence to glove utilization among healthcare workers was suboptimal. Gloves were overused and often misused. The major break in compliance with glove use was failure to change gloves between procedures on the same patient. Inappropriate glove use can increase the risk of cross transmission. It is unclear if modifications in glove use alter compliance with hand hygiene among healthcare workers. Gloving can reduce acquisition of microorganisms on the hands. However, gloving does not completely prevent contamination of the hands. Compliance with glove use among healthcare workers is poor. Gloves were also overused and often misused. Inappropriate glove use can increase the risk of cross transmission via contaminated gloved hands. There is still not enough evidence to prove the influence of glove use on adherence to hand hygiene. This review strengthens the recent suggestion on the use of gloves to reduce bacterial contamination. However, gloving does not completely prevent contamination, thus emphasizing the need for hand antisepsis before and after patient contact. Intervention to improve the use of gloves and hand hygiene compliance after gloving in the healthcare settings should be implemented. Further studies should target poor compliers with glove use and promote strategies that can be evaluated. The Joanna Briggs Institute.

Orientation and mobility training for partially-sighted older adults using an identification cane: a systematic review

PubMed Central

Ballemans, Judith; Kempen, Gertrudis IJM; Zijlstra, GA Rixt

2011-01-01

Objective: This study aimed to provide an overview of the development, content, feasibility, and effectiveness of existing orientation and mobility training programmes in the use of the identification cane. Data sources: A systematic bibliographic database search in PubMed, PsychInfo, ERIC, CINAHL and the Cochrane Library was performed, in combination with the expert consultation (n = 42; orientation and mobility experts), and hand-searching of reference lists. Review methods: Selection criteria included a description of the development, the content, the feasibility, or the effectiveness of orientation and mobility training in the use of the identification cane. Two reviewers independently agreed on eligibility and methodological quality. A narrative/qualitative data analysis method was applied to extract data from obtained documents. Results: The sensitive database search and hand-searching of reference lists revealed 248 potentially relevant abstracts. None met the eligibility criteria. Expert consultation resulted in the inclusion of six documents in which the information presented on the orientation and mobility training in the use of the identification cane was incomplete and of low methodological quality. Conclusion: Our review of the literature showed a lack of well-described protocols and studies on orientation and mobility training in identification cane use. PMID:21795405

Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories.

PubMed

Kuhn, Stefan; Schlörer, Nils E

2015-08-01

nmrshiftdb2 supports with its laboratory information management system the integration of an electronic lab administration and management into academic NMR facilities. Also, it offers the setup of a local database, while full access to nmrshiftdb2's World Wide Web database is granted. This freely available system allows on the one hand the submission of orders for measurement, transfers recorded data automatically or manually, and enables download of spectra via web interface, as well as the integrated access to prediction, search, and assignment tools of the NMR database for lab users. On the other hand, for the staff and lab administration, flow of all orders can be supervised; administrative tools also include user and hardware management, a statistic functionality for accounting purposes, and a 'QuickCheck' function for assignment control, to facilitate quality control of assignments submitted to the (local) database. Laboratory information management system and database are based on a web interface as front end and are therefore independent of the operating system in use. Copyright © 2015 John Wiley & Sons, Ltd.

Computerized literature reference system: use of an optical scanner and optical character recognition software.

PubMed

Lossef, S V; Schwartz, L H

1990-09-01

A computerized reference system for radiology journal articles was developed by using an IBM-compatible personal computer with a hand-held optical scanner and optical character recognition software. This allows direct entry of scanned text from printed material into word processing or data-base files. Additionally, line diagrams and photographs of radiographs can be incorporated into these files. A text search and retrieval software program enables rapid searching for keywords in scanned documents. The hand scanner and software programs are commercially available, relatively inexpensive, and easily used. This permits construction of a personalized radiology literature file of readily accessible text and images requiring minimal typing or keystroke entry.

Finding knowledge translation articles in CINAHL.

PubMed

Lokker, Cynthia; McKibbon, K Ann; Wilczynski, Nancy L; Haynes, R Brian; Ciliska, Donna; Dobbins, Maureen; Davis, David A; Straus, Sharon E

2010-01-01

The process of moving research into practice has a number of names including knowledge translation (KT). Researchers and decision makers need to be able to readily access the literature on KT for the field to grow and to evaluate the existing evidence. To develop and validate search filters for finding KT articles in the database Cumulative Index to Nursing and Allied Health (CINAHL). A gold standard database was constructed by hand searching and classifying articles from 12 journals as KT Content, KT Applications and KT Theory. Sensitivity, specificity, precision, and accuracy of the search filters. Optimized search filters had fairly low sensitivity and specificity for KT Content (58.4% and 64.9% respectively), while sensitivity and specificity increased for retrieving KT Application (67.5% and 70.2%) and KT Theory articles (70.4% and 77.8%). Search filter performance was suboptimal marking the broad base of disciplines and vocabularies used by KT researchers. Such diversity makes retrieval of KT studies in CINAHL difficult.

Systematic review of use of β-blockers in sepsis.

PubMed

Chacko, Cyril Jacob; Gopal, Shameer

2015-01-01

We proposed a review of present literature and systematic analysis of present literature to summarize the evidence on the use of β-blockers on the outcome of a patient with severe sepsis and septic shock. Medline, EMBASE, Cochrane Library were searched from 1946 to December 2013. The bibliography of all relevant articles was hand searched. Full-text search of the grey literature was done through the medical institution database. The database search identified a total of 1241 possible studies. The citation list was hand searched by both the authors. A total of 9 studies were identified. Most studies found a benefit from β-blocker administration in sepsis. This included improved heart rate (HR) control, decreased mortality and improvement in acid-base parameters. Chronic β-blocker usage in sepsis was also associated with improved mortality. The administration of β-blockers during sepsis was associated with better control of HR. The methodological quality of all the included studies, however, was poor. There is insufficient evidence to justify the routine use of β-blockers in sepsis. A large adequately powered multi-centered randomized controlled clinical trial is required to address the question on the efficacy of β-blocker usage in sepsis. This trial should also consider a number of important questions including the choice of β-blocker used, optimal dosing, timing of intervention, duration of intervention and discontinuation of the drug. Until such time based on the available evidence, there is no place for the use of β-blockers in sepsis in current clinical practice.

Audio stream classification for multimedia database search

NASA Astrophysics Data System (ADS)

Artese, M.; Bianco, S.; Gagliardi, I.; Gasparini, F.

2013-03-01

Search and retrieval of huge archives of Multimedia data is a challenging task. A classification step is often used to reduce the number of entries on which to perform the subsequent search. In particular, when new entries of the database are continuously added, a fast classification based on simple threshold evaluation is desirable. In this work we present a CART-based (Classification And Regression Tree [1]) classification framework for audio streams belonging to multimedia databases. The database considered is the Archive of Ethnography and Social History (AESS) [2], which is mainly composed of popular songs and other audio records describing the popular traditions handed down generation by generation, such as traditional fairs, and customs. The peculiarities of this database are that it is continuously updated; the audio recordings are acquired in unconstrained environment; and for the non-expert human user is difficult to create the ground truth labels. In our experiments, half of all the available audio files have been randomly extracted and used as training set. The remaining ones have been used as test set. The classifier has been trained to distinguish among three different classes: speech, music, and song. All the audio files in the dataset have been previously manually labeled into the three classes above defined by domain experts.

The Effect of Orthodontic Therapy on Periodontal Health: A Review of the Literature

PubMed Central

Alfuriji, Samah; Alhazmi, Nora; Alhamlan, Nasir; Al-Ehaideb, Ali; Alruwaithi, Moatazbellah; Alkatheeri, Nasser; Geevarghese, Amrita

2014-01-01

Objectives. This review aims to evaluate the effect of orthodontic therapy on periodontal health. Data. Original articles that reported on the effect of orthodontic therapy on periodontal health were included. The reference lists of potentially relevant review articles were also sought. Sources. A literature search was conducted using the databases, Medline, EMBASE, Cochrane Library, Web of Science, Google Scholar, and Scopus databases for relevant studies. The search was carried out by using a combined text and the MeSH search strategies: using the key words in different combinations: “periodontal disease,” “orthodontics” and “root resorption.” This was supplemented by hand-searching in peer-reviewed journals and cross-referenced with the articles accessed. Articles published only in English language were included. Letters to the Editor, historical reviews and unpublished articles were not sought. Conclusions. Within the limitations of the present literature review, it was observed that there is a very close inter-relationship between the periodontal health and the outcome of orthodontic therapy. PMID:24991214

Search strategies to identify information on adverse effects: a systematic review

PubMed Central

Golder, Su; Loke, Yoon

2009-01-01

Objectives: The review evaluated studies of electronic database search strategies designed to retrieve adverse effects data for systematic reviews. Methods: Studies of adverse effects were located in ten databases as well as by checking references, hand-searching, searching citations, and contacting experts. Two reviewers screened the retrieved records for potentially relevant papers. Results: Five thousand three hundred thirteen citations were retrieved, yielding 19 studies designed to develop or evaluate adverse effect filters, of which 3 met the inclusion criteria. All 3 studies identified highly sensitive search strategies capable of retrieving over 95% of relevant records. However, 1 study did not evaluate precision, while the level of precision in the other 2 studies ranged from 0.8% to 2.8%. Methodological issues in these papers included the relatively small number of records, absence of a validation set of records for testing, and limited evaluation of precision. Conclusions: The results indicate the difficulty of achieving highly sensitive searches for information on adverse effects with a reasonable level of precision. Researchers who intend to locate studies on adverse effects should allow for the amount of resources and time required to conduct a highly sensitive search. PMID:19404498

Gallbladder cancer.

PubMed

Gourgiotis, Stavros; Kocher, Hemant M; Solaini, Leonardo; Yarollahi, Arvin; Tsiambas, Evangelos; Salemis, Nikolaos S

2008-08-01

Gallbladder cancer (GC) is a relatively rare but highly lethal neoplasm. We review the epidemiology, etiology, pathology, symptoms, diagnosis, staging, treatment, and prognosis of GC. A Pubmed database search between 1971 and February 2007 was performed. All abstracts were reviewed and articles with GC obtained; further references were extracted by hand-searching the bibliography. The database search was done in the English language. The accurate etiology of GC remains unclear, while the symptoms associated with primary GC are not specific. Treatment with radical cholecystectomy is curative but possible in only 10% to 30% of patients. For patients whose cancer is an incidental finding on pathologic review, re-resection is indicated, where feasible, for all disease except T1a. Patients with advanced disease should receive palliative treatment. Laparoscopic cholecystectomy is contraindicated in the presence of GC. Prognosis generally is extremely poor. Improvements in the outcome of surgical resection have caused this approach to be re-evaluated, while the role of chemotherapy and radiotherapy remains controversial.

Complementary and Alternative Therapies for Autism Spectrum Disorder

PubMed Central

Fusar-Poli, Laura; Rocchetti, Matteo; Provenzani, Umberto; Barale, Francesco

2015-01-01

Background. Complementary and alternative medicine (CAM) represents a popular therapeutic option for patients with autism spectrum disorder (ASD). Unfortunately, there is a paucity of data regarding the efficacy of CAM in ASD. The aim of the present systematic review is to investigate trials of CAM in ASD. Material and Methods. We searched the following databases: MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, CINAHL, Psychology and Behavioral Sciences Collection, Agricola, and Food Science Source. Results. Our literature search identified 2687 clinical publications. After the title/abstract screening, 139 publications were obtained for detailed evaluation. After detailed evaluation 67 studies were included, from hand search of references we retrieved 13 additional studies for a total of 80. Conclusion. There is no conclusive evidence supporting the efficacy of CAM therapies in ASD. Promising results are reported for music therapy, sensory integration therapy, acupuncture, and massage. PMID:26064157

Is hand sewing comparable with stapling for anastomotic leakage after esophagectomy? A meta-analysis

PubMed Central

Liu, Quan-Xing; Min, Jia-Xin; Deng, Xu-Feng; Dai, Ji-Gang

2014-01-01

AIM: To compare the outcome of hand sewing and stapling for anastomotic leakage after esophagectomy. METHODS: A rigorous study protocol was established according to the recommendations of the Cochrane Collaboration. An electronic database search, hand search, and reference search were used to retrieve all randomized controlled trials that compared hand-sewn and mechanical esophagogastric anastomoses. RESULTS: This study included 15 randomized controlled trials with a total of 2337 patients. The results revealed that there was no significant difference in the incidence of anastomotic leakage between the methods [relative risk (RR) = 0.77, 95% confidence interval (CI): 0.57-1.04; P = 0.09], but a subgroup analysis yielded a significant difference for the sutured layer and year of publication (Ps < 0.05). There was also no significant difference in the incidence of postoperative mortality (RR = 1.52, 95%CI: 0.97-2.40; P = 0.07). However, the anastomotic strictures rate was increased in the stapler group compared with the hand-sewn group (RR = 1.45, 95%CI: 1.11-1.91; P < 0.01) in the end-to-side subgroup, while the incidence of anastomotic strictures was decreased (RR = 0.34, 95%CI: 0.16-0.76; P < 0.01) in the side-to-side subgroup. CONCLUSION: The stapler reduces the anastomotic leakage rate compared with hand sewing. End-to-side stapling increases the risk of anastomotic strictures, but side-to-side stapling decreases the risk. PMID:25493038

Nursing record systems: effects on nursing practice and health care outcomes.

PubMed

Currell, R; Urquhart, C

2003-01-01

A nursing record system is the record of care planned and/or given to individual patients/clients by qualified nurses or other caregivers under the direction of a qualified nurse. Nursing record systems may be an effective way of influencing nurse practice. To assess the effects of nursing record systems on nursing practice and patient outcomes. We searched The Cochrane Library, the EPOC trial register (October 2002), MEDLINE, Cinahl, Sigle, and databases of the Royal College of Nursing, King's Fund, the NHS Centre for Reviews and Dissemination, and the Institute of Electrical Engineers up to August 1999; and OCLC First Search, Department of Health database, NHS Register of Computer Applications and the Health Visitors' Association database up to the end of 1995. We hand searched the Journal of Nursing Administration (1971-1999), Computers in Nursing (1984-1999), Information Technology in Nursing (1989-1999) and reference lists of articles. We also hand searched the major health informatics conference proceedings. We contacted experts in the field of nursing informatics, suppliers of nursing computer systems, and relevant Internet groups. To update the review the Medline, Cinahl, British Nursing Index, Aslib Index to Theses databases were all searched from 1998 to 2002. The Journal of Nursing Administration, Computers in Nursing, Information Technology in Nursing were all hand searched up to 2002. The searches of the other databases and grey literature included in the original review, were not updated (except for Health Care Computing Conference and Med Info) as the original searches produced little relevant material. Randomised trials, controlled before and after studies and interrupted time series comparing one kind of nursing record system with another, in hospital, community or primary care settings. The participants were qualified nurses, students or health care assistants working under the direction of a qualified nurse and patients receiving care recorded and/or planned using nursing record systems. Two reviewers independently assessed trial quality and extracted data. Eight trials involving 1497 people were included. In three studies of client held records, there were no overall positive or negative effects, although some administrative benefits through fewer missing notes were suggested. A paediatric pain management sheet study showed a positive effect on the children's pain intensity. A computerised nursing care planning study showed a negative effect on documented nursing care planning, although two other computerised nursing information studies showed an increase in recording but no change in patient outcomes. Care planning took longer with these computerised systems, but the numbers of patients and nurses included in these studies was small. A controlled before-and-after study of two paper nursing record systems showed improvement in meeting documentation standards. No evidence was found of effects on practice attributable to changes in record systems. Although there is a paucity of studies of sufficient methodological rigour to yield reliable results in this area, it is clear from the literature that it is possible to set up randomised trials or other quasi-experimental designs needed to produce evidence for practice. The research undertaken so far may have suffered both from methodological problems and faulty hypotheses. Qualitative nursing research to explore the relationship between practice and information use, could be used as a precursor to the design and testing of nursing information systems.

Critical Assessment of Search Strategies in Systematic Reviews in Endodontics.

PubMed

Yaylali, Ibrahim Ethem; Alaçam, Tayfun

2016-06-01

The aim of this study was to perform an overview of literature search strategies in systematic reviews (SRs) published in 2 endodontic journals, Journal of Endodontics and International Endodontic Journal. A search was done by using the MEDLINE (PubMed interface) database to retrieve the articles published between January 1, 2000 and December 31, 2015. The last search was on January 10, 2016. All the SRs published in the 2 journals were retrieved and screened. Eligible SRs were assessed by using 11 questions about search strategies in the SRs that were adapted from 2 guidelines (ie, AMSTAR checklist and the Cochrane Handbook). A total of 83 SRs were retrieved by electronic search. Of these, 55 were from the Journal of Endodontics, and 28 were from the International Endodontic Journal. After screening, 2 SRs were excluded, and 81 SRs were included in the study. Some issues, such as search of grey literature and contact with study authors, were not fully reported (30% and 25%, respectively). On the other hand, some issues, such as the use of index terms and key words and search in at least 2 databases, were reported in most of the SRs (97% and 95%, respectively). The overall quality of the search strategy in both journals was 61%. No significant difference was found between the 2 journals in terms of evaluation criteria (P > .05). There exist areas for improving the quality of reporting of search strategies in SRs; for example, grey literature should be searched for unpublished studies, no language limitation should be applied to databases, and authors should make an attempt to contact the authors of included studies to obtain further relevant information. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Strategies for expanding health insurance coverage in vulnerable populations.

PubMed

Jia, Liying; Yuan, Beibei; Huang, Fei; Lu, Ying; Garner, Paul; Meng, Qingyue

2014-11-26

Health insurance has the potential to improve access to health care and protect people from the financial risks of diseases. However, health insurance coverage is often low, particularly for people most in need of protection, including children and other vulnerable populations. To assess the effectiveness of strategies for expanding health insurance coverage in vulnerable populations. We searched Cochrane Central Register of Controlled Trials (CENTRAL), part of The Cochrane Library. www.thecochranelibrary.com (searched 2 November 2012), PubMed (searched 1 November 2012), EMBASE (searched 6 July 2012), Global Health (searched 6 July 2012), IBSS (searched 6 July 2012), WHO Library Database (WHOLIS) (searched 1 November 2012), IDEAS (searched 1 November 2012), ISI-Proceedings (searched 1 November 2012),OpenGrey (changed from OpenSIGLE) (searched 1 November 2012), African Index Medicus (searched 1 November 2012), BLDS (searched 1 November 2012), Econlit (searched 1 November 2012), ELDIS (searched 1 November 2012), ERIC (searched 1 November 2012), HERDIN NeON Database (searched 1 November 2012), IndMED (searched 1 November 2012), JSTOR (searched 1 November 2012), LILACS(searched 1 November 2012), NTIS (searched 1 November 2012), PAIS (searched 6 July 2012), Popline (searched 1 November 2012), ProQuest Dissertation &Theses Database (searched 1 November 2012), PsycINFO (searched 6 July 2012), SSRN (searched 1 November 2012), Thai Index Medicus (searched 1 November 2012), World Bank (searched 2 November 2012), WanFang (searched 3 November 2012), China National Knowledge Infrastructure (CHKD-CNKI) (searched 2 November 2012).In addition, we searched the reference lists of included studies and carried out a citation search for the included studies via Web of Science to find other potentially relevant studies. Randomised controlled trials (RCTs), non-randomised controlled trials (NRCTs), controlled before-after (CBA) studies and Interrupted time series (ITS) studies that evaluated the effects of strategies on increasing health insurance coverage for vulnerable populations. We defined strategies as measures to improve the enrolment of vulnerable populations into health insurance schemes. Two categories and six specified strategies were identified as the interventions. At least two review authors independently extracted data and assessed the risk of bias. We undertook a structured synthesis. We included two studies, both from the United States. People offered health insurance information and application support by community-based case managers were probably more likely to enrol their children into health insurance programmes (risk ratio (RR) 1.68, 95% confidence interval (CI) 1.44 to 1.96, moderate quality evidence) and were probably more likely to continue insuring their children (RR 2.59, 95% CI 1.95 to 3.44, moderate quality evidence). Of all the children that were insured, those in the intervention group may have been insured quicker (47.3 fewer days, 95% CI 20.6 to 74.0 fewer days, low quality evidence) and parents may have been more satisfied on average (satisfaction score average difference 1.07, 95% CI 0.72 to 1.42, low quality evidence).In the second study applications were handed out in emergency departments at hospitals, compared to not handing out applications, and may have had an effect on enrolment (RR 1.5, 95% CI 1.03 to 2.18, low quality evidence). Community-based case managers who provide health insurance information, application support, and negotiate with the insurer probably increase enrolment of children in health insurance schemes. However, the transferability of this intervention to other populations or other settings is uncertain. Handing out insurance application materials in hospital emergency departments may help increase the enrolment of children in health insurance schemes. Further studies evaluating the effectiveness of different strategies for expanding health insurance coverage in vulnerable population are needed in different settings, with careful attention given to study design.

search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information

PubMed Central

2013-01-01

Background Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. Results We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. Conclusions search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/. PMID:23452691

search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information.

PubMed

Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Siążnik, Artur

2013-03-01

Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user's query, advanced data searching based on the specified user's query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/.

Accredited hand surgery fellowship Web sites: analysis of content and accessibility.

PubMed

Trehan, Samir K; Morrell, Nathan T; Akelman, Edward

2015-04-01

To assess the accessibility and content of accredited hand surgery fellowship Web sites. A list of all accredited hand surgery fellowships was obtained from the online database of the American Society for Surgery of the Hand (ASSH). Fellowship program information on the ASSH Web site was recorded. All fellowship program Web sites were located via Google search. Fellowship program Web sites were analyzed for accessibility and content in 3 domains: program overview, application information/recruitment, and education. At the time of this study, there were 81 accredited hand surgery fellowships with 169 available positions. Thirty of 81 programs (37%) had a functional link on the ASSH online hand surgery fellowship directory; however, Google search identified 78 Web sites. Three programs did not have a Web site. Analysis of content revealed that most Web sites contained contact information, whereas information regarding the anticipated clinical, research, and educational experiences during fellowship was less often present. Furthermore, information regarding past and present fellows, salary, application process/requirements, call responsibilities, and case volume was frequently lacking. Overall, 52 of 81 programs (64%) had the minimal online information required for residents to independently complete the fellowship application process. Hand fellowship program Web sites could be accessed either via the ASSH online directory or Google search, except for 3 programs that did not have Web sites. Although most fellowship program Web sites contained contact information, other content such as application information/recruitment and education, was less frequently present. This study provides comparative data regarding the clinical and educational experiences outlined on hand fellowship program Web sites that are of relevance to residents, fellows, and academic hand surgeons. This study also draws attention to various ways in which the hand surgery fellowship application process can be made more user-friendly and efficient. Copyright © 2015 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

Short dental implants: an emerging concept in implant treatment.

PubMed

Al-Hashedi, Ashwaq Ali; Taiyeb Ali, Tara Bai; Yunus, Norsiah

2014-06-01

Short implants have been advocated as a treatment option in many clinical situations where the use of conventional implants is limited. This review outlines the effectiveness and clinical outcomes of using short implants as a valid treatment option in the rehabilitation of edentulous atrophic alveolar ridges. Initially, an electronic search was performed on the following databases: Medline, PubMed, Embase, Cochrane Database of Systematic Reviews, and DARE using key words from January 1990 until May 2012. An additional hand search was included for the relevant articles in the following journals: International Journal of Oral and Maxillofacial Implants, Clinical Oral Implants Research, Journal of Clinical Periodontology, International Journal of Periodontics, Journal of Periodontology, and Clinical Implant Dentistry and Related Research. Any relevant papers from the journals' references were hand searched. Articles were included if they provided detailed data on implant length, reported survival rates, mentioned measures for implant failure, were in the English language, involved human subjects, and researched implants inserted in healed atrophic ridges with a follow-up period of at least 1 year after implant-prosthesis loading. Short implants demonstrated a high rate of success in the replacement of missing teeth in especially atrophic alveolar ridges. The advanced technology and improvement of the implant surfaces have encouraged the success of short implants to a comparable level to that of standard implants. However, further randomized controlled clinical trials and prospective studies with longer follow-up periods are needed.

Timing of Debridement and Infection Rates in Open Fractures of the Hand

PubMed Central

Ketonis, Constantinos; Dwyer, Joseph; Ilyas, Asif M.

2016-01-01

Background: Literature on open fracture infections has focused primarily on long bones, with limited guidelines available for open hand fractures. In this study, we systematically review the available hand surgery literature to determine infection rates and the effect of debridement timing and antibiotic administration. Methods: Searches of the MEDLINE, EMBASE, and Cochrane computerized literature databases and manual bibliography searches were performed. Descriptive/quantitative data were extracted, and a meta-analysis of different patient cohorts and treatment modalities was performed to compare infection rates. Results: The initial search yielded 61 references. Twelve articles (4 prospective, 8 retrospective) on open hand fractures were included (1669 open fractures). There were 77 total infections (4.6%): 61 (4.4%) of 1391 patients received preoperative antibiotics and 16 (9.4%) of 171 patients did not receive antibiotics. In 7 studies (1106 open fractures), superficial infections (requiring oral antibiotics only) accounted for 86%, whereas deep infections (requiring operative debridement) accounted for 14%. Debridement within 6 hours of injury (2 studies, 188 fractures) resulted in a 4.2% infection rate, whereas debridement within 12 hours of injury (1 study, 193 fractures) resulted in a 3.6% infection rate. Two studies found no correlation of infection and timing to debridement. Conclusions: Overall, the infection rate after open hand fracture remains relatively low. Correlation does exist between the administration of antibiotics and infection, but the majority of infections can be treated with antibiotics alone. Timing of debridement, has not been shown to alter infection rates. PMID:28344521

[The theme of disaster in health care: profile of technical and scientific production in the specialized database on disasters of the Virtual Health Library - VHL].

PubMed

Rocha, Vania; Ximenes, Elisa Francioli; Carvalho, Mauren Lopes de; Alpino, Tais de Moura Ariza; Freitas, Carlos Machado de

2014-09-01

In the specialized database of the Virtual Health Library (VHL), the DISASTER database highlights the importance of the theme for the health sector. The scope of this article is to identify the profiles of technical and scientific publications in the specialized database. Based on systematic searches and the analysis of results it is possible to determine: the type of publication; the main topics addressed; the most common type of disasters mentioned in published materials, countries and regions as subjects, historic periods with the most publications and the current trend of publications. When examining the specialized data in detail, it soon becomes clear that the number of major topics is very high, making a specific search process in this database a challenging exercise. On the other hand, it is encouraging that the disaster topic is discussed and assessed in a broad and diversified manner, associated with different aspects of the natural and social sciences. The disaster issue requires the production of interdisciplinary knowledge development to reduce the impacts of disasters and for risk management. In this way, since the health sector is a interdisciplinary area, it can contribute to knowledge production.

Traditional manual acupuncture combined with rehabilitation therapy for shoulder hand syndrome after stroke within the Chinese healthcare system: a systematic review and meta-analysis.

PubMed

Peng, Le; Zhang, Chao; Zhou, Lan; Zuo, Hong-Xia; He, Xiao-Kuo; Niu, Yu-Ming

2018-04-01

To investigate the effectiveness of traditional manual acupuncture combined with rehabilitation therapy versus rehabilitation therapy alone for shoulder hand syndrome after stroke. PubMed, EMBASE, the Cochrane Library, Chinese Biomedicine Database, China National Knowledge Infrastructure, VIP Information Database, Wan Fang Database and reference lists of the eligible studies were searched up to July 2017 for relevant studies. Randomized controlled trials that compared the combined effects of traditional manual acupuncture and rehabilitation therapy to rehabilitation therapy alone for shoulder hand syndrome after stroke were included. Two reviewers independently screened the searched records, extracted the data and assessed risk of bias of the included studies. The treatment effect sizes were pooled in a meta-analysis using RevMan 5.3 software. A total of 20 studies involving 1918 participants were included in this study. Compared to rehabilitation therapy alone, the combined therapy significantly reduced pain on the visual analogue scale and improved limb movement on the Fugl-Meyer Assessment scale and the performance of activities of daily living (ADL) on the Barthel Index scale or Modified Barthel Index scale. Of these, the visual analogue scale score changes were significantly higher (mean difference = 1.49, 95% confidence interval = 1.15-1.82, P < 0.00001) favoring the combined therapy after treatment, with severe heterogeneity ( I 2  = 71%, P = 0.0005). Current evidence suggests that traditional manual acupuncture integrated with rehabilitation therapy is more effective in alleviating pain, improving limb movement and ADL. However, considering the relatively low quality of available evidence, further rigorously designed and large-scale randomized controlled trials are needed to confirm the results.

Approach to traumatic hand injuries for primary care physicians.

PubMed

Cheung, Kevin; Hatchell, Alexandra; Thoma, Achilleas

2013-06-01

To review the initial management of common traumatic hand injuries seen by primary care physicians. Current clinical evidence and literature identified through MEDLINE electronic database searches was reviewed. Expert opinion was used to supplement recommendations for areas with little evidence. Primary care physicians must routinely manage patients with acute traumatic hand injuries. In the context of a clinical case, we review the assessment, diagnosis, and initial management of common traumatic hand injuries. The presentation and management of nail bed injuries, fingertip amputations, mallet fingers, hand fractures, tendon lacerations, bite injuries, and infectious tenosynovitis will also be discussed. The principles of managing traumatic hand injuries involve the reduction and immobilization of fractures, obtaining post-reduction x-ray scans, obtaining soft tissue coverage, preventing and treating infection, and ensuring tetanus prophylaxis. Proper assessment and management of traumatic hand injuries is essential to prevent substantial long-term morbidity in this generally otherwise healthy population. Early recognition of injuries that require urgent or emergent referral to a hand surgeon is critical.

Gluten-Free and Casein-Free Diets in the Treatment of Autism Spectrum Disorders: A Systematic Review

ERIC Educational Resources Information Center

Mulloy, Austin; Lang, Russell; O'Reilly, Mark; Sigafoos, Jeff; Lancioni, Giulio; Rispoli, Mandy

2010-01-01

This paper systematically reviews research on the effects of gluten-free and/or casein-free (GFCF) diets in the treatment of ASD. Database, hand, and ancestry searches identified 15 articles for review. Each study was analyzed and summarized in terms of (a) participants, (b) specifics of the intervention, (c) dependent variables, (d) results, and…

A comparison of two search methods for determining the scope of systematic reviews and health technology assessments.

PubMed

Forsetlund, Louise; Kirkehei, Ingvild; Harboe, Ingrid; Odgaard-Jensen, Jan

2012-01-01

This study aims to compare two different search methods for determining the scope of a requested systematic review or health technology assessment. The first method (called the Direct Search Method) included performing direct searches in the Cochrane Database of Systematic Reviews (CDSR), Database of Abstracts of Reviews of Effects (DARE) and the Health Technology Assessments (HTA). Using the comparison method (called the NHS Search Engine) we performed searches by means of the search engine of the British National Health Service, NHS Evidence. We used an adapted cross-over design with a random allocation of fifty-five requests for systematic reviews. The main analyses were based on repeated measurements adjusted for the order in which the searches were conducted. The Direct Search Method generated on average fewer hits (48 percent [95 percent confidence interval {CI} 6 percent to 72 percent], had a higher precision (0.22 [95 percent CI, 0.13 to 0.30]) and more unique hits than when searching by means of the NHS Search Engine (50 percent [95 percent CI, 7 percent to 110 percent]). On the other hand, the Direct Search Method took longer (14.58 minutes [95 percent CI, 7.20 to 21.97]) and was perceived as somewhat less user-friendly than the NHS Search Engine (-0.60 [95 percent CI, -1.11 to -0.09]). Although the Direct Search Method had some drawbacks such as being more time-consuming and less user-friendly, it generated more unique hits than the NHS Search Engine, retrieved on average fewer references and fewer irrelevant results.

Outcome Measurement in the Treatment of Spasmodic Dysphonia: A Systematic Review of the Literature.

PubMed

Rumbach, Anna; Aiken, Patrick; Novakovic, Daniel

2018-04-11

The aim of this review was to systematically identify all available studies reporting outcomes measures to assess treatment outcomes for people with spasmodic dysphonia (SD). Full-text journal articles were identified through searches of PubMed, Embase, CINAHL, and Cochrane databases and hand searching of journals. A total of 4,714 articles were retrieved from searching databases; 1,165 were duplicates. Titles and abstracts of 3,549 were screened, with 171 being selected for full-text review. During full-text review, 101 articles were deemed suitable for inclusion. An additional 24 articles were identified as suitable for inclusion through a hand search of reference lists. Data were extracted from 125 studies. A total of 220 outcome measures were identified. Considered in reference to the World Health Organization International Classification of Functioning, Disability and Health (ICF), the majority of outcomes were measured at a Body Function level (n = 212, 96%). Outcomes that explored communication and participation in everyday life and attitudes toward communication (ie, activity and participation domains) were infrequent (n = 8; 4%). Quality of life, a construct not measured within the ICF, was also captured by four outcome measures. No instruments evaluating communication partners' perspectives or burden/disability were identified. The outcome measures used in SD treatment studies are many and varied. The outcome measures identified predominately measure constructs within the Body Functions component of the ICF. In order to facilitate data synthesis across trials, the development of a core outcome set is recommended. Crown Copyright © 2018. Published by Elsevier Inc. All rights reserved.

A highly sensitive search strategy for clinical trials in Literatura Latino Americana e do Caribe em Ciências da Saúde (LILACS) was developed.

PubMed

Manríquez, Juan J

2008-04-01

Systematic reviews should include as many articles as possible. However, many systematic reviews use only databases with high English language content as sources of trials. Literatura Latino Americana e do Caribe em Ciências da Saúde (LILACS) is an underused source of trials, and there is not a validated strategy for searching clinical trials to be used in this database. The objective of this study was to develop a sensitive search strategy for clinical trials in LILACS. An analytical survey was performed. Several single and multiple-term search strategies were tested for their ability to retrieve clinical trials in LILACS. Sensitivity, specificity, and accuracy of each single and multiple-term strategy were calculated using the results of a hand-search of 44 Chilean journals as gold standard. After combining the most sensitive, specific, and accurate single and multiple-term search strategy, a strategy with a sensitivity of 97.75% (95% confidence interval [CI]=95.98-99.53) and a specificity of 61.85 (95% CI=61.19-62.51) was obtained. LILACS is a source of trials that could improve systematic reviews. A new highly sensitive search strategy for clinical trials in LILACS has been developed. It is hoped this search strategy will improve and increase the utilization of LILACS in future systematic reviews.

Applying psychological frameworks of behaviour change to improve healthcare worker hand hygiene: a systematic review.

PubMed

Srigley, J A; Corace, K; Hargadon, D P; Yu, D; MacDonald, T; Fabrigar, L; Garber, G

2015-11-01

Despite the importance of hand hygiene in preventing transmission of healthcare-associated infections, compliance rates are suboptimal. Hand hygiene is a complex behaviour and psychological frameworks are promising tools to influence healthcare worker (HCW) behaviour. (i) To review the effectiveness of interventions based on psychological theories of behaviour change to improve HCW hand hygiene compliance; (ii) to determine which frameworks have been used to predict HCW hand hygiene compliance. Multiple databases and reference lists of included studies were searched for studies that applied psychological theories to improve and/or predict HCW hand hygiene. All steps in selection, data extraction, and quality assessment were performed independently by two reviewers. The search yielded 918 citations; seven met eligibility criteria. Four studies evaluated hand hygiene interventions based on psychological frameworks. Interventions were informed by goal setting, control theory, operant learning, positive reinforcement, change theory, the theory of planned behaviour, and the transtheoretical model. Three predictive studies employed the theory of planned behaviour, the transtheoretical model, and the theoretical domains framework. Interventions to improve hand hygiene adherence demonstrated efficacy but studies were at moderate to high risk of bias. For many studies, it was unclear how theories of behaviour change were used to inform the interventions. Predictive studies had mixed results. Behaviour change theory is a promising tool for improving hand hygiene; however, these theories have not been extensively examined. Our review reveals a significant gap in the literature and indicates possible avenues for novel research. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Are opioid antagonists effective in reducing self-injury in adults with intellectual disability? A systematic review.

PubMed

Roy, A; Roy, M; Deb, S; Unwin, G; Roy, A

2015-01-01

Self-injury in people with intellectual disability (ID) may be due to variety of factors both environmental and biological. As the drive in UK is to manage people with ID and problem behaviours in the community, it is important to critically examine all treatment options available. As abnormalities in the endogenous opioid system may be a factor in some people with ID, we undertook a systematic review to evaluate the evidence for the effectiveness of opioid antagonists. Four electronic databases were searched for relevant journal articles. In addition, cross-referencing of pertinent reviews and a hand search for articles in major international ID journals between the years 2010 and 2012 was carried out to ensure that all relevant articles were identified. We also searched databases for unpublished clinical trials to overcome publication bias. Each database was searched up to present (February 2013) with no restrictions on the date of publication. The search terms consisted of broad expressions used to describe ID and autistic spectrum disorder as well as terms relating to opioid antagonists and specific drugs. All studies identified by the electronic database search and hand search were examined on the basis of title alone for relevance and duplication. The abstracts of the remaining papers were then scrutinised against the inclusion criteria. Where abstracts failed to provide adequate information, the full texts for these papers were obtained. All the full texts were then evaluated against the inclusion proforma. Two reviewers carried out all the stages of the process independently. The reviewers met to discuss their selections and where disagreements arose, these were settled by discussion with a member of the study group. Data from each study meeting the inclusion criteria was extracted on a pre-piloted data extraction form. The quality of each study was further assessed using the Jadad scale, a tool developed to assess the quality of randomised controlled trials. Out of 10 randomised control trials eight reported a reduction in the frequency of self-injurious behaviour. This meant that 62 participants out of 124 (50%) showed an improvement of which 61 were statistically significant. Forty-nine participants had autism. Eleven (9%) had minor side-effects. The improvement was more marked in people with severe and profound ID and was not affected by the coexistence of autism. This review suggests that some people respond to opioid antagonists with a reduction in self-injury but the trials do not predict who they may be. Future research may identify this sub-group when opioid antagonists may prove to be a useful addition in the pharmacotherapy of self-injury. © 2014 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

Data, Metadata - Who Cares?

NASA Astrophysics Data System (ADS)

Baumann, Peter

2013-04-01

There is a traditional saying that metadata are understandable, semantic-rich, and searchable. Data, on the other hand, are big, with no accessible semantics, and just downloadable. Not only has this led to an imbalance of search support form a user perspective, but also underneath to a deep technology divide often using relational databases for metadata and bespoke archive solutions for data. Our vision is that this barrier will be overcome, and data and metadata become searchable likewise, leveraging the potential of semantic technologies in combination with scalability technologies. Ultimately, in this vision ad-hoc processing and filtering will not distinguish any longer, forming a uniformly accessible data universe. In the European EarthServer initiative, we work towards this vision by federating database-style raster query languages with metadata search and geo broker technology. We present our approach taken, how it can leverage OGC standards, the benefits envisaged, and first results.

The effectiveness of home hand exercise programmes in rheumatoid arthritis: a systematic review.

PubMed

Hammond, Alison; Prior, Yeliz

2016-09-01

Rheumatoid arthritis (RA) commonly reduces hand function. We systematically reviewed trials to investigate effects of home hand exercise programmes on hand symptoms and function in RA. We searched: Medline (1946-), AMED, CINAHL, Physiotherapy Evidence Database, OT Seeker, the Cochrane Library, ISI Web of Science from inception to January 2016. Nineteen trials were evaluated. Only three were randomized controlled trials with a low risk of bias (n = 665). Significant short-term improvements occurred in hand function, pain and grip strength, with long-term improvements in hand and upper limb function and pinch strength. Heterogeneity of outcome measures meant meta-analysis was not possible. Evaluation of low and moderate risk of bias trials indicated high-intensity home hand exercise programmes led to better short-term outcomes than low-intensity programmes. Such programmes are cost-effective. Further research is required to evaluate methods of helping people with RA maintain long-term home hand exercise. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Supported Decision-Making: Implications from Positive Psychology for Assessment and Intervention in Rehabilitation and Employment.

PubMed

Uyanik, Hatice; Shogren, Karrie A; Blanck, Peter

2017-12-01

Purpose This article reviews existing literature on positive psychology, supported decision-making (SDM), employment, and disability. It examines interventions and assessments that have been empirically evaluated for the enhancement of decision-making and overall well-being of people with disabilities. Additionally, conceptual themes present in the literature were explored. Methods A systematic review was conducted across two databases (ERIC and PsychINFO) using various combination of keywords of 'disabilit*', work rehabilitation and employment terms, positive psychology terms, and SDM components. Seven database searches were conducted with diverse combinations of keywords, which identified 1425 results in total to be screened for relevance using their titles and abstracts. Database search was supplemented with hand searches of oft-cited journals, ancestral search, and supplemental search from grey literature. Results Only four studies were identified in the literature targeting SDM and positive psychology related constructs in the employment and job development context. Results across the studies indicated small to moderate impacts of the assessment and interventions on decision-making and engagement outcomes. Conceptually there are thematic areas of potential overlap, although they are limited in the explicit integration of theory in supported decision-making, positive psychology, disability, and employment. Conclusion Results suggest a need for additional scholarship in this area that focuses on theory development and integration as well as empirical work. Such work should examine the potential utility of considering positive psychological interventions when planning for SDM in the context of career development activities to enhance positive outcomes related to decision-making, self-determination, and other positive psychological constructs.

Contextual cueing of tactile search is coded in an anatomical reference frame.

PubMed

Assumpção, Leonardo; Shi, Zhuanghua; Zang, Xuelian; Müller, Hermann J; Geyer, Thomas

2018-04-01

This work investigates the reference frame(s) underlying tactile context memory, a form of statistical learning in a tactile (finger) search task. In this task, if a searched-for target object is repeatedly encountered within a stable spatial arrangement of task-irrelevant distractors, detecting the target becomes more efficient over time (relative to nonrepeated arrangements), as learned target-distractor spatial associations come to guide tactile search, thus cueing attention to the target location. Since tactile search displays can be represented in several reference frames, including multiple external and an anatomical frame, in Experiment 1 we asked whether repeated search displays are represented in tactile memory with reference to an environment-centered or anatomical reference frame. In Experiment 2, we went on examining a hand-centered versus anatomical reference frame of tactile context memory. Observers performed a tactile search task, divided into a learning and test session. At the transition between the two sessions, we introduced postural manipulations of the hands (crossed ↔ uncrossed in Expt. 1; palm-up ↔ palm-down in Expt. 2) to determine the reference frame of tactile contextual cueing. In both experiments, target-distractor associations acquired during learning transferred to the test session when the placement of the target and distractors was held constant in anatomical, but not external, coordinates. In the latter, RTs were even slower for repeated displays. We conclude that tactile contextual learning is coded in an anatomical reference frame. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

A framework for designing hand hygiene educational interventions in schools.

PubMed

Appiah-Brempong, Emmanuel; Harris, Muriel J; Newton, Samuel; Gulis, Gabriel

2018-03-01

Hygiene education appears to be the commonest school-based intervention for preventing infectious diseases, especially in the developing world. Nevertheless, there remains a gap in literature regarding a school-specific theory-based framework for designing a hand hygiene educational intervention in schools. We sought to suggest a framework underpinned by psychosocial theories towards bridging this knowledge gap. Furthermore, we sought to propound a more comprehensive definition of hand hygiene which could guide the conceptualisation of hand hygiene interventions in varied settings. Literature search was guided by a standardized tool and literature was retrieved on the basis of a predetermined inclusion criteria. Databases consulted include PubMed, ERIC, and EBSCO host (Medline, CINAHL, PsycINFO, etc.). Evidence bordering on a theoretical framework to aid the design of school-based hand hygiene educational interventions is summarized narratively. School-based hand hygiene educational interventions seeking to positively influence behavioural outcomes could consider enhancing psychosocial variables including behavioural capacity, attitudes and subjective norms (normative beliefs and motivation to comply). A framework underpinned by formalized psychosocial theories has relevance and could enhance the design of hand hygiene educational interventions, especially in schools.

Addressing unwarranted clinical variation: A rapid review of current evidence.

PubMed

Harrison, Reema; Manias, Elizabeth; Mears, Stephen; Heslop, David; Hinchcliff, Reece; Hay, Liz

2018-05-15

Unwarranted clinical variation (UCV) can be described as variation that can only be explained by differences in health system performance. There is a lack of clarity regarding how to define and identify UCV and, once identified, to determine whether it is sufficiently problematic to warrant action. As such, the implementation of systemic approaches to reducing UCV is challenging. A review of approaches to understand, identify, and address UCV was undertaken to determine how conceptual and theoretical frameworks currently attempt to define UCV, the approaches used to identify UCV, and the evidence of their effectiveness. Rapid evidence assessment (REA) methodology was used. A range of text words, synonyms, and subject headings were developed for the major concepts of unwarranted clinical variation, standards (and deviation from these standards), and health care environment. Two electronic databases (Medline and Pubmed) were searched from January 2006 to April 2017, in addition to hand searching of relevant journals, reference lists, and grey literature. Results were merged using reference-management software (Endnote) and duplicates removed. Inclusion criteria were independently applied to potentially relevant articles by 3 reviewers. Findings were presented in a narrative synthesis to highlight key concepts addressed in the published literature. A total of 48 relevant publications were included in the review; 21 articles were identified as eligible from the database search, 4 from hand searching published work and 23 from the grey literature. The search process highlighted the voluminous literature reporting clinical variation internationally; yet, there is a dearth of evidence regarding systematic approaches to identifying or addressing UCV. Wennberg's classification framework is commonly cited in relation to classifying variation, but no single approach is agreed upon to systematically explore and address UCV. The instances of UCV that warrant investigation and action are largely determined at a systems level currently, and stakeholder engagement in this process is limited. Lack of consensus on an evidence-based definition for UCV remains a substantial barrier to progress in this field. © 2018 John Wiley & Sons, Ltd.

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison.

PubMed

Hahn, Lars; Leimeister, Chris-André; Ounit, Rachid; Lonardi, Stefano; Morgenstern, Burkhard

2016-10-01

Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set. We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this algorithm is called rasbhari. Depending on the application at hand, rasbhari can either minimize the overlap complexity of pattern sets, maximize their sensitivity in database searching or minimize the variance of the number of pattern-based matches in alignment-free sequence comparison. We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches. In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets that we previously used. Finally, we used rasbhari to generate patterns for short read classification with CLARK-S. Here too, the sensitivity of the results could be improved, compared to the default patterns of the program. We integrated rasbhari into Spaced Words; the source code of rasbhari is freely available at http://rasbhari.gobics.de/.

The Effects of Surgical Hand Scrubbing Protocols on Skin Integrity and Surgical Site Infection Rates: A Systematic Review.

PubMed

Liu, Liang Qin; Mehigan, Sinead

2016-05-01

This systematic review aimed to critically appraise and synthesize updated evidence regarding the effect of surgical-scrub techniques on skin integrity and the incidence of surgical site infections. Databases searched include the Cumulative Index to Nursing and Allied Health Literature, MEDLINE, Embase, and Cochrane Central. Our review was limited to eight peer-reviewed, randomized controlled trials and two nonrandomized controlled trials published in English from 1990 to 2015. Comparison models included traditional hand scrubbing with chlorhexidine gluconate or povidone-iodine against alcohol-based hand rubbing, scrubbing with a brush versus without a brush, and detergent-based antiseptics alone versus antiseptics incorporating alcohol solutions. Evidence showed that hand rubbing techniques are as effective as traditional scrubbing and seem to be better tolerated. Hand rubbing appears to cause less skin damage than traditional scrub protocols, and scrub personnel tolerated brushless techniques better than scrubbing using a brush. Copyright © 2016 AORN, Inc. Published by Elsevier Inc. All rights reserved.

Effects of therapy for dysphagia in Parkinson's disease: systematic review.

PubMed

Baijens, Laura W J; Speyer, Renée

2009-03-01

This systematic review explores the effects of dysphagia treatment for Parkinson's disease. The review includes rehabilitative, surgical, pharmacologic, and other treatments. Only oropharyngeal dysphagia is selected for this literature search, excluding dysphagia due to esophageal or gastric disorders. The effects of deep brain stimulation on dysphagia are not included. In general, the literature concerning dysphagia treatment in Parkinson's disease is rather limited. Most effect studies show diverse methodologic problems. Multiple case studies and trials are identified by searching biomedical literature databases PubMed and Embase, and by hand-searching reference lists. The conclusions of most studies cannot be compared with one another because of heterogeneous therapy methods and outcome measures. Further research based on randomized controlled trials to determine the effectiveness of different therapies for dysphagia in Parkinson's disease is required.

Hand osteoarthritis: an epidemiological perspective.

PubMed

Kalichman, Leonid; Hernández-Molina, Gabriela

2010-06-01

Hand osteoarthritis (OA) is a highly prevalent condition with a wide spectrum of clinical presentations. We review herein the prevalence, impact on hand function, and various risk factors related to hand OA. PubMed and MEDLINE databases (1950-2009) were searched for the keywords: "hand," "hand osteoarthritis," "distal interphalangeal," "proximal interphalangeal," "metacarpophalangeal," and "carpometacarpal." Published material emphasizing cohort, cross-sectional, and case-control studies regarding epidemiology, clinical features, functional impairment, and associated risk factors of hand OA were included. Hand OA is a heterogeneous, age- and gender-dependent disorder, occurring more frequently in women over 50 years of age. In the elderly population, the prevalence of radiographic hand OA can reach 80%. OA has a strong genetic predisposition, apparently gender- and phenotype-specific. A history of heavy manual labor or a repetitive use of the hand also has been linked to OA. Other variables such as weight, smoking, joint hyperlaxity, age of menarche, bone and cartilage mineralization factors, grip strength, and handedness may play a role. Symptomatic hand OA may cause functional impairment due to loss of strength, thus limiting the individual's ability to perform daily tasks. Several risk factors for hand OA have been identified; however, their interrelationship is not clearly understood. The development of preventive strategies and future research goals is needed. Copyright 2010 Elsevier Inc. All rights reserved.

Performance Factors Related to the Different Tennis Backhand Groundstrokes: A Review

PubMed Central

Genevois, Cyril; Reid, Machar; Rogowski, Isabelle; Crespo, Miguel

2015-01-01

The backhand is one of the two basic groundstrokes in tennis and can be played both with one or two hands, with topspin or backspin. Despite its variety of derivatives, the scientific literature describing the backhand groundstroke production has not been reviewed as extensively as with the serve and the forehand. The purpose of this article is to review the research describing the mechanics of one and two-handed backhands, with a critical focus on its application to clinicians and coaches. One hundred and thirty four articles satisfied a key word search (tennis, backhand) in relevant databases and manual search, with only 61 of those articles considered directly relevant to our review. The consensus of this research supports major differences between both the one- and two-handed strokes, chiefly about their respective contributions of trunk rotation and the role of the non-dominant upper extremity. Two-handed backhand strokes rely more on trunk rotation for the generation of racquet velocity, while the one-handed backhands utilize segmental rotations of the upper limb to develop comparable racquet speeds. There remains considerable scope for future research to examine expertise, age and/or gender-related kinematic differences to strengthen the practitioner’s understanding of the key mechanical considerations that may shape the development of proficient backhand strokes. Key points One-and two-handed backhands require different motor coordination Two-handed backhand strokes rely more on trunk rotation for racquet velocity generation, whereas one-handed backhand strokes rely more on segmental rotations of the upper limb Players using a two-handed backhand should learn early a slice one-handed backhand because of the different co-ordination pattern involved Equipment scaling is a great tool for coaches to learn early proper one-handed backhand strokes Future research related to the interaction between backhand technique, gender and skill level is needed PMID:25729308

The role of child sexual abuse in the etiology of substance-related disorders.

PubMed

Maniglio, Roberto

2011-01-01

To elucidate the role of child sexual abuse in the etiology of substance-related disorders, a systematic review of the several articles on the childhood sexual abuse-related risk for developing substance problems in adolescence or adulthood is provided. Seven databases were searched, supplemented with hand-search of reference lists. Six reviews, including 200 studies, were included. Results indicate that child sexual abuse is a statistically significant, although general and nonspecific, risk factor for substance problems. Other biological and psychosocial variables contribute to substance-related disorders, with sexual abuse conferring additional risk, either as a distal, indirect cause or as a proximal, direct cause. Recommendations for future research are provided.

Topological materials discovery using electron filling constraints

NASA Astrophysics Data System (ADS)

Chen, Ru; Po, Hoi Chun; Neaton, Jeffrey B.; Vishwanath, Ashvin

2018-01-01

Nodal semimetals are classes of topological materials that have nodal-point or nodal-line Fermi surfaces, which give them novel transport and topological properties. Despite being highly sought after, there are currently very few experimental realizations, and identifying new materials candidates has mainly relied on exhaustive database searches. Here we show how recent studies on the interplay between electron filling and nonsymmorphic space-group symmetries can guide the search for filling-enforced nodal semimetals. We recast the previously derived constraints on the allowed band-insulator fillings in any space group into a new form, which enables effective screening of materials candidates based solely on their space group, electron count in the formula unit, and multiplicity of the formula unit. This criterion greatly reduces the computation load for discovering topological materials in a database of previously synthesized compounds. As a demonstration, we focus on a few selected nonsymmorphic space groups which are predicted to host filling-enforced Dirac semimetals. Of the more than 30,000 entires listed, our filling criterion alone eliminates 96% of the entries before they are passed on for further analysis. We discover a handful of candidates from this guided search; among them, the monoclinic crystal Ca2Pt2Ga is particularly promising.

Review of telehealth stuttering management.

PubMed

Lowe, Robyn; O'Brian, Sue; Onslow, Mark

2013-01-01

Telehealth is the use of communication technology to provide health care services by means other than typical in-clinic attendance models. Telehealth is increasingly used for the management of speech, language and communication disorders. The aim of this article is to review telehealth applications to stuttering management. We conducted a search of peer-reviewed literature for the past 20 years using the Institute for Scientific Information Web of Science database, PubMed: The Bibliographic Database and a search for articles by hand. Outcomes for telehealth stuttering treatment were generally positive, but there may be a compromise of treatment efficiency with telehealth treatment of young children. Our search found no studies dealing with stuttering assessment procedures using telehealth models. No economic analyses of this delivery model have been reported. This review highlights the need for continued research about telehealth for stuttering management. Evidence from research is needed to inform the efficacy of assessment procedures using telehealth methods as well as guide the development of improved treatment procedures. Clinical and technical guidelines are urgently needed to ensure that the evolving and continued use of telehealth to manage stuttering does not compromise the standards of care afforded with standard in-clinic models.

Basal Cell Carcinoma of the Dorsal Hand: An Update and Comprehensive Review of the Literature.

PubMed

Loh, Tiffany Y; Rubin, Ashley G; Brian Jiang, Shang I

2016-04-01

Excessive ultraviolet radiation (UVR) exposure is the primary predisposing factor for basal cell carcinoma (BCC). However, surprisingly, BCCs occur very rarely on the dorsal hand, which is subject to intense sun exposure, and their infrequent presentation in this location suggests that other factors besides UVR may play a role in BCC pathogenesis. Because dorsal hand BCCs are uncommon, knowledge of their characteristics is limited, and more data are needed to describe their clinical presentation and treatment. To perform an updated review of the literature on the management of dorsal hand BCCs. The authors conducted a comprehensive literature review by searching the PubMed database with the key phrases "basal cell carcinoma dorsal hand," "basal cell carcinoma hand," and "basal cell carcinoma finger," and "basal cell carcinoma thumb." The authors identified 176 cases of dorsal hand BCCs in the literature, 120 of which had sufficient data for analysis. Only 4 cases were treated with Mohs micrographic surgery (MMS). The authors present 14 additional cases of dorsal hand BCCs treated with MMS. Basal cell carcinomas on the dorsal hand occur infrequently, and potential risk factors include being a male of white descent and personal history of skin cancer. Mohs micrographic surgery seems to be an effective treatment method.

Loneliness: a concept analysis.

PubMed

Bekhet, Abir K; Zauszniewski, Jaclene A; Nakhla, Wagdy E

2008-01-01

Loneliness is a universal human experience recognized since the dawn of time, yet it is unique for every individual. Loneliness can lead to both depression and low self-esteem. This article explicates the concept of loneliness through the examination of its conceptual definition and uses, defining attributes, related concepts, and empirical referents. Literature review using hand search and database were used as sources of information. Because loneliness is commonly encountered in nursing situations, the information provided will serve as a framework for assessment, planning, intervention, and evaluation of clients.

Tobacco smoking and hand eczema - is there an association?

PubMed

Sørensen, Jennifer A; Clemmensen, Kim K; Nixon, Rosemary L; Diepgen, Thomas L; Agner, Tove

2015-12-01

Numerous risk factors have been suggested for hand eczema. This systematic review evaluates the association between tobacco smoking and hand eczema. To review the literature systematically on the association between smoking and hand eczema. The PubMed and EMBASE databases were searched up to 27 January 2015 for articles on the association between tobacco smoking and hand eczema, including human studies in English and German only. Experimental studies, studies on tobacco allergy, case reports, reviews and studies on second-hand smoking were excluded. Twenty articles were included. Among studies in occupational settings, three of seven found a statistically significant positive association between tobacco smoking and hand eczema prevalence rate, as did four of eight population-based studies. The association was stronger for studies in occupational settings than for population-based studies. No studies reported tobacco to be a clear protective factor for hand eczema. Two of five studies regarding severity found a positive association between smoking and hand eczema severity. Overall, the data indicate that smoking may cause an increased frequency of hand eczema, particularly in high-risk occupations. However, data from studies controlling for other risk factors are conflicting, and few prospective studies are available. Studies controlling for other risk factors are needed, and information regarding the diagnosis of subclasses of hand eczema, as well as severity, may be important. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

searchSCF: Using MongoDB to Enable Richer Searches of Locally Hosted Science Data Repositories

NASA Astrophysics Data System (ADS)

Knosp, B.

2016-12-01

Science teams today are in the unusual position of almost having too much data available to them. Modern sensors and models are capable of outputting terabytes of data per day, which can make it difficult to find specific subsets of data. The sheer size of files can also make it time consuming to retrieve this big data from national data archive centers. Thus, many science teams choose to store what data they can on their local systems, but they are not always equipped with tools to help them intelligently organize and search their data. In its local data repository, the Aura Microwave Limb Sounder (MLS) science team at NASA's Jet Propulsion Laboratory has collected over 300TB of atmospheric science data from 71 missions/models that aid in validation, algorithm development, and research activities. When the project began, the team developed a MySQL database to aid in data queries, but this database was only designed to keep track of MLS and a few ancillary data sets, leving much of the data uncatalogued. The team has also seen database query time rise over the life of the mission. Even though the MLS science team's data holdings are not the size of a national data center's, team members still need tools to help them discover and utilize the data that they have on-hand. Over the past year, members of the science team have been looking for solutions to (1) store information on all the data sets they have collected in a single database, (2) store more metadata about each data file, (3) develop queries that can find relationships among these disparate data types, and (4) plug any new functions developed around this database into existing analysis, visualization, and web tools, transparently to users. In this presentation, I will discuss the searchSCF package that is currently under development. This package includes a NoSQL database management system (MongoDB) and a set of Python tools that both ingests data into the database and supports user queries. I will also highlight case studies of how this system could be used by the MLS science team, and how it could be implemented by other science teams with local data repositories.

The Role of Information Provision in Economic Evaluations of Newborn Bloodspot Screening: A Systematic Review.

PubMed

Wright, Stuart J; Jones, Cheryl; Payne, Katherine; Dharni, Nimarta; Ulph, Fiona

2015-12-01

The extent to which economic evaluations have included the healthcare resource and outcome-related implications of information provision in national newborn bloodspot screening programmes (NBSPs) is not currently known. To identify if, and how, information provision has been incorporated into published economic evaluations of NBSPs. A systematic review of economic evaluations of NBSPs (up to November 2014) was conducted. Three electronic databases were searched (Ovid: Medline, Embase, CINAHL) using an electronic search strategy combining a published economic search filter with terms related to national NBSPs and screening-related technologies. These electronic searches were supplemented by searching the NHS Economic Evaluations Database (NHS EED) and hand-searching identified study reference lists. The results were tabulated and summarised as part of a narrative synthesis. A total of 27 economic evaluations [screening-related technologies (n = 11) and NBSPs (n = 16)] were identified. The majority of economic evaluations did not quantify the impact of information provision in terms of healthcare costs or outcomes. Five studies did include an estimate of the time cost associated with information provision. Four studies included a value to reflect the disutility associated with parental anxiety caused by false-positive results, which was used as a proxy for the impact of imperfect information. A limited evidence base currently quantifies the impact of information provision on the healthcare costs and impact on the users of NBSPs; the parents of newborns. We suggest that economic evaluations of expanded NBSPs need to take account of information provision otherwise the impact on healthcare costs and the outcomes for newborns and their parents may be underestimated.

Nursing record systems: effects on nursing practice and health care outcomes.

PubMed

Currell, R; Wainwright, P; Urquhart, C

2000-01-01

A nursing record system is the record of care planned and/or given to individual patients/clients by qualified nurses or other caregivers under the direction of a qualified nurse. Nursing record systems may be an effective way of influencing nurse practice. To assess the effects of nursing record systems on nursing practice and patient outcomes. We searched The Cochrane Library, MEDLINE, Cinahl, Sigle, and databases of the Royal College of Nursing, King's Fund, the NHS Centre for Reviews and Dissemination, and the Institute of Electrical Engineers up to August 1999; and OCLC First Search, Department of Health database, NHS Register of Computer Applications and the Health Visitors' Association database up to the end of 1995. We hand searched the Journal of Nursing Administration (1971-1999), Computers in Nursing (1984-1999), Information Technology in Nursing (1989-1999) and reference lists of articles. We also hand searched the major health informatics conference proceedings. We contacted experts in the field of nursing informatics, suppliers of nursing computer systems, and relevant Internet groups. Randomised trials, controlled before and after studies and interrupted time series comparing one kind of nursing record system with another, in hospital, community or primary care settings. The participants were qualified nurses, students or health care assistants working under the direction of a qualified nurse and patients receiving care recorded and/or planned using nursing record systems. Two reviewers independently assessed trial quality and extracted data. Six trials involving 1407 people were included. In three studies of client held records, there were no overall positive or negative effects, although some administrative benefits through fewer missing notes were suggested. A paediatric pain management sheet study showed a positive effect on the children's pain intensity. A computerised nursing care planning study showed a negative effect on documented nursing care planning. A controlled before-and-after study of two paper nursing record systems showed improvement in meeting documentation standards. No evidence was found of effects on practice attributable to changes in record systems. Although there is a paucity of studies of sufficient methodological rigour to yield reliable results in this area, it is clear from the literature that it is possible to set up randomised trials or other quasi-experimental designs needed to produce evidence for practice. The research undertaken so far may have suffered both from methodological problems and faulty hypotheses.

Data augmentation-assisted deep learning of hand-drawn partially colored sketches for visual search

PubMed Central

Muhammad, Khan; Baik, Sung Wook

2017-01-01

In recent years, image databases are growing at exponential rates, making their management, indexing, and retrieval, very challenging. Typical image retrieval systems rely on sample images as queries. However, in the absence of sample query images, hand-drawn sketches are also used. The recent adoption of touch screen input devices makes it very convenient to quickly draw shaded sketches of objects to be used for querying image databases. This paper presents a mechanism to provide access to visual information based on users’ hand-drawn partially colored sketches using touch screen devices. A key challenge for sketch-based image retrieval systems is to cope with the inherent ambiguity in sketches due to the lack of colors, textures, shading, and drawing imperfections. To cope with these issues, we propose to fine-tune a deep convolutional neural network (CNN) using augmented dataset to extract features from partially colored hand-drawn sketches for query specification in a sketch-based image retrieval framework. The large augmented dataset contains natural images, edge maps, hand-drawn sketches, de-colorized, and de-texturized images which allow CNN to effectively model visual contents presented to it in a variety of forms. The deep features extracted from CNN allow retrieval of images using both sketches and full color images as queries. We also evaluated the role of partial coloring or shading in sketches to improve the retrieval performance. The proposed method is tested on two large datasets for sketch recognition and sketch-based image retrieval and achieved better classification and retrieval performance than many existing methods. PMID:28859140

BioCarian: search engine for exploratory searches in heterogeneous biological databases.

PubMed

Zaki, Nazar; Tennakoon, Chandana

2017-10-02

There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com . We have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

Update in Hospice and Palliative Care.

PubMed

Gray, Nathan A; Horton, Jay R; Dionne-Odom, J Nicholas; Smith, Cardinale B; Johnson, Kimberly S

2016-05-01

The goal of this update in hospice and palliative care is to summarize and critique research published between January 1 and December 31, 2014 that has a high potential for impact on clinical practice. To identify articles we hand searched 22 leading journals, the Cochrane Database of Systematic Reviews, and Fast Article Critical Summaries for Clinicians in Palliative Care. We also performed a PubMed keyword search using the terms "hospice" and "palliative care." We ranked candidate articles based on study quality, appeal to a breadth of palliative care clinicians, and potential for impact on clinical practice. In this manuscript we have summarized the findings of eight articles with the highest ratings and make recommendations for clinical practice based on the strength of the resulting evidence.

Dental insurance: A systematic review.

PubMed

Garla, Bharath Kumar; Satish, G; Divya, K T

2014-12-01

To review uses of finance in dentistry. A search of 25 electronic databases and World Wide Web was conducted. Relevant journals were hand searched and further information was requested from authors. Inclusion criteria were a predefined hierarchy of evidence and objectives. Study validity was assessed with checklists. Two reviewers independently screened sources, extracted data, and assessed validity. Insurance has come of ages and has become the mainstay of payment in many developed countries. So much so that all the alternative forms of payment which originated as an alternative to fee for service now depend on insurance at one point or the other. Fee for service is still the major form of payment in many developing countries including India. It is preferred in many instances since the payment is made immediately.

Adjacency and Proximity Searching in the Science Citation Index and Google

DTIC Science & Technology

2005-01-01

major database search engines , including commercial S&T database search engines (e.g., Science Citation Index (SCI), Engineering Compendex (EC...PubMed, OVID), Federal agency award database search engines (e.g., NSF, NIH, DOE, EPA, as accessed in Federal R&D Project Summaries), Web search Engines (e.g...searching. Some database search engines allow strict constrained co- occurrence searching as a user option (e.g., OVID, EC), while others do not (e.g., SCI

Do the contents of working memory capture attention? Yes, but cognitive control matters.

PubMed

Han, Suk Won; Kim, Min-Shik

2009-10-01

There has been a controversy on whether working memory can guide attentional selection. Some researchers have reported that the contents of working memory guide attention automatically in visual search (D. Soto, D. Heinke, G. W. Humphreys, & M. J. Blanco, 2005). On the other hand, G.F. Woodman and S. J. Luck (2007) reported that they could not find any evidence of attentional capture by working memory. In the present study, we tried to find an integrative explanation for the different sets of results. We report evidence for attentional capture by working memory, but this effect was eliminated when search was perceptually demanding or the onset of the search was delayed long enough for cognitive control of search to be implemented under particular conditions. We suggest that perceptual difficulty and the time course of cognitive control as important factors that determine when information in working memory influences attention. PsycINFO Database Record (c) 2009 APA, all rights reserved.

[A systematic evaluation of application of the web-based cancer database].

PubMed

Huang, Tingting; Liu, Jialin; Li, Yong; Zhang, Rui

2013-10-01

In order to support the theory and practice of the web-based cancer database development in China, we applied a systematic evaluation to assess the development condition of the web-based cancer databases at home and abroad. We performed computer-based retrieval of the Ovid-MEDLINE, Springerlink, EBSCOhost, Wiley Online Library and CNKI databases, the papers of which were published between Jan. 1995 and Dec. 2011, and retrieved the references of these papers by hand. We selected qualified papers according to the pre-established inclusion and exclusion criteria, and carried out information extraction and analysis of the papers. Eventually, searching the online database, we obtained 1244 papers, and checking the reference lists, we found other 19 articles. Thirty-one articles met the inclusion and exclusion criteria and we extracted the proofs and assessed them. Analyzing these evidences showed that the U.S.A. counted for 26% in the first place. Thirty-nine percent of these web-based cancer databases are comprehensive cancer databases. As for single cancer databases, breast cancer and prostatic cancer are on the top, both counting for 10% respectively. Thirty-two percent of the cancer database are associated with cancer gene information. For the technical applications, MySQL and PHP applied most widely, nearly 23% each.

Comet: an open-source MS/MS sequence database search tool.

PubMed

Eng, Jimmy K; Jahan, Tahmina A; Hoopmann, Michael R

2013-01-01

Proteomics research routinely involves identifying peptides and proteins via MS/MS sequence database search. Thus the database search engine is an integral tool in many proteomics research groups. Here, we introduce the Comet search engine to the existing landscape of commercial and open-source database search tools. Comet is open source, freely available, and based on one of the original sequence database search tools that has been widely used for many years. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Database Search Engines: Paradigms, Challenges and Solutions.

PubMed

Verheggen, Kenneth; Martens, Lennart; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

2016-01-01

The first step in identifying proteins from mass spectrometry based shotgun proteomics data is to infer peptides from tandem mass spectra, a task generally achieved using database search engines. In this chapter, the basic principles of database search engines are introduced with a focus on open source software, and the use of database search engines is demonstrated using the freely available SearchGUI interface. This chapter also discusses how to tackle general issues related to sequence database searching and shows how to minimize their impact.

Review of the evidence on the use of arbitration or consensus within breast screening: A systematic scoping review.

PubMed

Hackney, L; Szczepura, A; Moody, L; Whiteman, B

2017-05-01

A systematic scoping review was undertaken to establish the evidence base on arbitration and consensus in mammography reporting. Database searches were supplemented with hand searching of peer-reviewed journals, citation tracking, key author searching, grey literature and personal contact with experts. A 3-stage process was utilised to screen a large volume of literature (601) against the inclusion and exclusion criteria. 26 papers were retained. A lack of guidance and underpinning evidence to inform how best to use arbitration or consensus to resolve discordant reads. In particular, a lack of prospective studies to determine effectiveness in real-life clinical settings. The insufficiency of follow-up or reporting of true interval cancers compromised the ability to conclude the effectiveness of the processes. Copyright © 2017 The College of Radiographers. Published by Elsevier Ltd. All rights reserved.

The contribution of nurses to incident disclosure: a narrative review.

PubMed

Harrison, Reema; Birks, Yvonne; Hall, Jill; Bosanquet, Kate; Harden, Melissa; Iedema, Rick

2014-02-01

To explore (a) how nurses feel about disclosing patient safety incidents to patients, (b) the current contribution that nurses make to the process of disclosing patient safety incidents to patients and (c) the barriers that nurses report as inhibiting their involvement in disclosure. A systematic search process was used to identify and select all relevant material. Heterogeneity in study design of the included articles prohibited a meta-analysis and findings were therefore synthesised in a narrative review. A range of text words, synonyms and subject headings were developed in conjunction with the York Centre for Reviews and Dissemination and used to undertake a systematic search of electronic databases (MEDLINE; EMBASE; CENTRAL; PsycINFO; Health Management and Information Consortium; CINAHL; ASSIA; Science Citation Index; Social Science Citation Index; Cochrane Database of Systematic Reviews; Database of Abstracts of Reviews of Effects; Health Technology Assessment Database; Health Systems Evidence; PASCAL; LILACS). Retrieval of studies was restricted to those published after 1980. Further data sources were: websites, grey literature, research in progress databases, hand-searching of relevant journals and author contact. The title and abstract of each citation was independently screened by two reviewers and disagreements resolved by consensus or consultation with a third person. Full text articles retrieved were further screened against the inclusion and exclusion criteria then checked by a second reviewer (YB). Relevant data were extracted and findings were synthesised in a narrative empirical synthesis. The systematic search and selection process identified 15 publications which included 11 unique studies that emerged from a range of locations. Findings suggest that nurses currently support both physicians and patients through incident disclosure, but may be ill-prepared to disclose incidents independently. Barriers to nurse involvement included a lack of opportunities for education and training, and the multiple and sometimes conflicting roles within nursing. Numerous potential benefits were identified that may result from nurses having a greater contribution to the disclosure process, but the provision of support and training is essential to overcome the reported barriers faced by nurses internationally. Copyright © 2013 Elsevier Ltd. All rights reserved.

An approach in building a chemical compound search engine in oracle database.

PubMed

Wang, H; Volarath, P; Harrison, R

2005-01-01

A searching or identifying of chemical compounds is an important process in drug design and in chemistry research. An efficient search engine involves a close coupling of the search algorithm and database implementation. The database must process chemical structures, which demands the approaches to represent, store, and retrieve structures in a database system. In this paper, a general database framework for working as a chemical compound search engine in Oracle database is described. The framework is devoted to eliminate data type constrains for potential search algorithms, which is a crucial step toward building a domain specific query language on top of SQL. A search engine implementation based on the database framework is also demonstrated. The convenience of the implementation emphasizes the efficiency and simplicity of the framework.

Sample size determination for bibliographic retrieval studies

PubMed Central

Yao, Xiaomei; Wilczynski, Nancy L; Walter, Stephen D; Haynes, R Brian

2008-01-01

Background Research for developing search strategies to retrieve high-quality clinical journal articles from MEDLINE is expensive and time-consuming. The objective of this study was to determine the minimal number of high-quality articles in a journal subset that would need to be hand-searched to update or create new MEDLINE search strategies for treatment, diagnosis, and prognosis studies. Methods The desired width of the 95% confidence intervals (W) for the lowest sensitivity among existing search strategies was used to calculate the number of high-quality articles needed to reliably update search strategies. New search strategies were derived in journal subsets formed by 2 approaches: random sampling of journals and top journals (having the most high-quality articles). The new strategies were tested in both the original large journal database and in a low-yielding journal (having few high-quality articles) subset. Results For treatment studies, if W was 10% or less for the lowest sensitivity among our existing search strategies, a subset of 15 randomly selected journals or 2 top journals were adequate for updating search strategies, based on each approach having at least 99 high-quality articles. The new strategies derived in 15 randomly selected journals or 2 top journals performed well in the original large journal database. Nevertheless, the new search strategies developed using the random sampling approach performed better than those developed using the top journal approach in a low-yielding journal subset. For studies of diagnosis and prognosis, no journal subset had enough high-quality articles to achieve the expected W (10%). Conclusion The approach of randomly sampling a small subset of journals that includes sufficient high-quality articles is an efficient way to update or create search strategies for high-quality articles on therapy in MEDLINE. The concentrations of diagnosis and prognosis articles are too low for this approach. PMID:18823538

Interventions for maintaining nasogastric feeding after stroke: An integrative review of effectiveness and acceptability.

PubMed

Mahoney, Catherine; Veitch, Linda

2018-02-01

To investigate the effectiveness and acceptability of interventions for maintaining nasogastric tubes in adult stroke patients. Internationally, incidence of cerebral vascular disease continues to increase and stroke is the largest cause of complex disability in adults. Dysphagia is common following a stroke which necessitates feeding via a nasogastric tube. Nasogastric tubes are not well tolerated by stroke patients and may be frequently dislodged. Hence, interventions such as tape, the nasal bridle/loop or hand mittens may be used to maintain nasogastric tube position. However, evidence around the effectiveness and acceptability of these interventions has not been reviewed and synthesised. Integrative literature review. Database searches in MEDLINE, PubMed, CINAHL, Scopus, Cochrane and EMBASE; manual reference list searches. Seven studies met the eligibility criteria and were included in the review. Evidence for the effectiveness of nasal bridle/loop and hand mittens to maintain nasogastric tube position in patients after a stroke is spare and methodologically poor, and especially limited around hand mittens use. There is insufficient evidence about the acceptability of both nasal bridle/loop and hand mittens among stroke patients. Current clinical practice is underpinned by assumptions around the acceptability of nasal bridle/loop and hand mittens to secure nasogastric tubes. This results in reliance on consensual judgement between professional, patients and their families to guide their use among individuals with dysphagia after stroke. Further research is required to assess the effectiveness of hand mittens and acceptability of both nasal bridle/loop and hand mittens among stroke patients to inform guideline development. Given the lack of evidence on the acceptability of hand mittens and nasal bridle/loop among stroke patients to inform evidence-based guidelines and protocols, healthcare professionals should reach consensus on their use by exercising clinical judgement and through consultation with patients (if possible) and their families. © 2017 John Wiley & Sons Ltd.

The Impact of Online Bibliographic Databases on Teaching and Research in Political Science.

ERIC Educational Resources Information Center

Reichel, Mary

The availability of online bibliographic databases greatly facilitates literature searching in political science. The advantages to searching databases online include combination of concepts, comprehensiveness, multiple database searching, free-text searching, currency, current awareness services, document delivery service, and convenience.…

Poor quality evidence suggests that failure rates for atraumatic restorative treatment and conventional amalgam are similar.

PubMed

Hurst, Dominic

2012-06-01

The Medline, Cochrane CENTRAL, Biomed Central, Database of Open Access Journals (DOAJ), OpenJ-Gate, Bibliografia Brasileira de Odontologia (BBO), LILACS, IndMed, Sabinet, Scielo, Scirus (Medicine), OpenSIGLE and Google Scholar databases were searched. Hand searching was performed for journals not indexed in the databases. References of included trials were checked. Prospective clinical trials with test and control groups with a follow up of at least one year were included. Data abstraction was conducted independently and clinical and methodologically homogeneous data were pooled using a fixed-effects model. Eighteen trials were included. From these 32 individual dichotomous datasets were extracted and analysed. The majority of the results show no differences between both types of intervention. A high risk of selection-, performance-, detection- and attrition bias was identified. Existing research gaps are mainly due to lack of trials and small sample size. The current evidence indicates that the failure rate of high-viscosity GIC/ART restorations is not higher than, but similar to that of conventional amalgam fillings after periods longer than one year. These results are in line with the conclusions drawn during the original systematic review. There is a high risk that these results are affected by bias, and thus confirmation by further trials with suitably high numbers of participants is needed.

Wavelet domain textual coding of Ottoman script images

NASA Astrophysics Data System (ADS)

Gerek, Oemer N.; Cetin, Enis A.; Tewfik, Ahmed H.

1996-02-01

Image coding using wavelet transform, DCT, and similar transform techniques is well established. On the other hand, these coding methods neither take into account the special characteristics of the images in a database nor are they suitable for fast database search. In this paper, the digital archiving of Ottoman printings is considered. Ottoman documents are printed in Arabic letters. Witten et al. describes a scheme based on finding the characters in binary document images and encoding the positions of the repeated characters This method efficiently compresses document images and is suitable for database research, but it cannot be applied to Ottoman or Arabic documents as the concept of character is different in Ottoman or Arabic. Typically, one has to deal with compound structures consisting of a group of letters. Therefore, the matching criterion will be according to those compound structures. Furthermore, the text images are gray tone or color images for Ottoman scripts for the reasons that are described in the paper. In our method the compound structure matching is carried out in wavelet domain which reduces the search space and increases the compression ratio. In addition to the wavelet transformation which corresponds to the linear subband decomposition, we also used nonlinear subband decomposition. The filters in the nonlinear subband decomposition have the property of preserving edges in the low resolution subband image.

Interventions to improve patient hand hygiene: a systematic review.

PubMed

Srigley, J A; Furness, C D; Gardam, M

2016-09-01

Nosocomial pathogens may be acquired by patients via their own unclean hands, but there has been relatively little emphasis on patient hand hygiene as a tool for preventing healthcare-associated infections (HCAIs). The aim of this systematic review was to determine the efficacy of patient hand hygiene interventions in reducing HCAIs and improving patient hand hygiene rates compared to usual care. Electronic databases and grey literature were searched to August 2014. Experimental and quasi-experimental studies were included if they evaluated a patient hand hygiene intervention conducted in an acute or chronic healthcare facility and included HCAI incidence and/or patient hand hygiene rates as an outcome. All steps were performed independently by two investigators. Ten studies were included, most of which were uncontrolled before-after studies (N=8). The majority of interventions (N=7) were multi-modal, with components similar to healthcare worker hand hygiene programmes, including education, reminders, audit and feedback, and provision of hand hygiene products. Six studies reported HCAI outcomes and four studies assessed patient hand hygiene rates; all demonstrated improvements but were at moderate to high risk of bias. In conclusion, interventions to improve patient hand hygiene may reduce the incidence of HCAIs and improve hand hygiene rates, but the quality of evidence is low. Future studies should use stronger designs and be more selective in their choice of outcomes. Copyright © 2016 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

How does feedback from patients impact upon healthcare student clinical skill development and learning? A systematic review.

PubMed

Finch, Emma; Lethlean, Jennifer; Rose, Tanya; Fleming, Jennifer; Theodoros, Deborah; Cameron, Ashley; Coleman, Adele; Copland, David; McPhail, Steven M

2018-03-01

A key feature of health professionals' training, irrespective of discipline, is the acquisition and application of clinical and communication skills. Despite this, little is known about the potential role of patient feedback on this process. This systematic review aimed to answer the question: How does feedback from patients impact upon healthcare student clinical skill development and learning? Systematic review of published literature. Electronic databases were searched for studies that explored the effects of patient feedback on student learning and were published before March 2016. Eligible articles underwent methodological evaluation using the McMaster University Critical Evaluation Forms and data extraction. A total of 237 articles were retrieved following searches of electronic databases and hand searches of reference lists. Twelve (7 quantitative, 2 qualitative, 3 mixed methods) studies met the inclusion criteria. Eleven studies reported that patient feedback improved students' clinical skills. Minimal research has explored the impact of patient feedback on student learning. The research to date suggests that direct feedback from patients may be beneficial for the development of students' communication and clinical skills; however, the wide variety of evaluation methods and the lack of validated tools for patients to provide feedback suggest that further exploration is warranted.

Consistency and accuracy of indexing systematic review articles and meta-analyses in medline.

PubMed

Wilczynski, Nancy L; Haynes, R Brian

2009-09-01

Systematic review articles support the advance of science and translation of research evidence into healthcare practice. Inaccurate retrieval from medline could limit access to reviews. To determine the quality of indexing systematic reviews and meta-analyses in medline. The Clinical Hedges Database, containing the results of a hand search of 161 journals, was used to test medline indexing terms for their ability to retrieve systematic reviews that met predefined methodologic criteria (labelled as 'pass' review articles) and reviews that reported a meta-analysis. The Clinical Hedges Database contained 49 028 articles; 753 were 'pass' review articles (552 with a meta-analysis). In total 758 review articles (independent of whether they passed) reported a meta-analysis. The search strategy that retrieved the highest number of 'pass' systematic reviews achieved a sensitivity of 97.1%. The publication type 'meta analysis' had a false positive rate of 5.6% (95% CI 3.9 to 7.6), and false negative rate of 0.31% (95% CI 0.26 to 0.36) for retrieving systematic reviews that reported a meta-analysis. Inaccuracies in indexing systematic reviews and meta-analyses in medline can be partly overcome by a 5-term search strategy. Introducing a publication type for systematic reviews of the literature could improve retrieval performance.

Tone as a health concept: An analysis.

PubMed

McDowall, Donald; Emmanuel, Elizabeth; Grace, Sandra; Chaseling, Marilyn

2017-11-01

Concept analysis. This paper is a report on the analysis of the concept of tone in chiropractic. The purpose of this paper is to clarify the concept of tone as originally understood by Daniel David Palmer from 1895 to 1914 and to monitor its evolution over time. Data was sourced from Palmer's original work, published between 1895 and 1914. A literature search from 1980 to 2016 was also performed on the online databases CINHAL, PubMed and Scopus with key terms including 'tone', 'chiropractic', 'Palmer', 'vitalism', 'health', 'homeostasis', 'holism' and 'wellness'. Finally hand-searches were conducted through chiropractic books and professional literature from 1906 to 1980 for any references to 'tone'. Rodgers' evolutionary method of analysis was used to categorise the data in relation to the surrogates, attributes, references, antecedents and consequences of tone. A total of 49 references were found: five from publications by Palmer; three from the database searches, and; the remaining 41 from professional books, trade journals and websites. There is no clear interpretation of tone in the contemporary chiropractic literature. Tone is closely aligned with functional neurology and can be understood as an interface between the metaphysical and the biomedical. Using the concept of tone as a foundation for practice could strengthen the identity of the chiropractic profession. Copyright © 2017 Elsevier Ltd. All rights reserved.

ATtRACT-a database of RNA-binding proteins and associated motifs.

PubMed

Giudice, Girolamo; Sánchez-Cabo, Fátima; Torroja, Carlos; Lara-Pezzi, Enrique

2016-01-01

RNA-binding proteins (RBPs) play a crucial role in key cellular processes, including RNA transport, splicing, polyadenylation and stability. Understanding the interaction between RBPs and RNA is key to improve our knowledge of RNA processing, localization and regulation in a global manner. Despite advances in recent years, a unified non-redundant resource that includes information on experimentally validated motifs, RBPs and integrated tools to exploit this information is lacking. Here, we developed a database named ATtRACT (available athttp://attract.cnic.es) that compiles information on 370 RBPs and 1583 RBP consensus binding motifs, 192 of which are not present in any other database. To populate ATtRACT we (i) extracted and hand-curated experimentally validated data from CISBP-RNA, SpliceAid-F, RBPDB databases, (ii) integrated and updated the unavailable ASD database and (iii) extracted information from Protein-RNA complexes present in Protein Data Bank database through computational analyses. ATtRACT provides also efficient algorithms to search a specific motif and scan one or more RNA sequences at a time. It also allows discoveringde novomotifs enriched in a set of related sequences and compare them with the motifs included in the database.Database URL:http:// attract. cnic. es. © The Author(s) 2016. Published by Oxford University Press.

Is there a difference between child self-ratings and parent proxy-ratings of the quality of life of children with a diagnosis of attention-deficit hyperactivity disorder (ADHD)? A systematic review of the literature.

PubMed

Galloway, Helen; Newman, Emily

2017-03-01

There are contemporary indicators that parent proxy-ratings and child self-ratings of a child's quality of life (QoL) are not interchangeable. This review examines dual informant studies to assess parent-child agreement on the QoL of children with attention-deficit/hyperactivity disorder. A systematic search of four major databases (PsycINFO, MEDLINE, EMBASE and Cochrane databases) was completed, and related peer-reviewed journals were hand-searched. Studies which reported quantitative QoL ratings for matched parent and child dyads were screened in accordance with relevant inclusion and exclusion criteria. Key findings were extracted from thirteen relevant studies, which were rated for conformity to the recommendations of an adapted version of the STROBE statement guidelines for observational studies. In the majority of studies reviewed, children rated their QoL more highly than their parents. There was some evidence for greater agreement on the physical health domain than psychosocial domains.

Are Bibliographic Management Software Search Interfaces Reliable?: A Comparison between Search Results Obtained Using Database Interfaces and the EndNote Online Search Function

ERIC Educational Resources Information Center

Fitzgibbons, Megan; Meert, Deborah

2010-01-01

The use of bibliographic management software and its internal search interfaces is now pervasive among researchers. This study compares the results between searches conducted in academic databases' search interfaces versus the EndNote search interface. The results show mixed search reliability, depending on the database and type of search…

Educational Quality of YouTube Videos in Thumb Exercises for Carpometacarpal Osteoarthritis: A Search on Current Practice.

PubMed

Villafañe, Jorge Hugo; Cantero-Tellez, Raquel; Valdes, Kristin; Usuelli, Federico Giuseppe; Berjano, Pedro

2017-09-01

Conservative treatments are commonly performed therapeutic interventions for the management of carpometacarpal (CMC) joint osteoarthritis (OA). Physical and occupational therapies are starting to use video-based online content as both a patient teaching tool and a source for treatment techniques. YouTube is a popular video-sharing website that can be accessed easily. The purpose of this study was to analyze the quality of content and potential sources of bias in videos available on YouTube pertaining to thumb exercises for CMC OA. The YouTube video database was systematically searched using the search term thumb osteoarthritis and exercises from its inception to March 10, 2017. Authors independently selected videos, conducted quality assessment, and extracted results. A total of 832 videos were found using the keywords. Of these, 10 videos clearly demonstrated therapeutic exercise for the management of CMC OA. In addition, the top-ranked video found by performing a search of "views" was a video with more than 121 863 views uploaded in 2015 that lasted 12.33 minutes and scored only 2 points on the Global Score for Educational Value rating scale. Most of the videos viewed that described conservative interventions for CMC OA management have a low level of evidence to support their use. Although patients and novice hand therapists are using YouTube and other online resources, videos that are produced by expert hand therapists are scarce.

Enablement in health care context: a concept analysis.

PubMed

Hudon, Catherine; St-Cyr Tribble, Denise; Bravo, Gina; Poitras, Marie-Eve

2011-02-01

The enablement process is defined as a professional intervention aiming to recognize, support and emphasize the patient's capacity to have control over her or his health and life. The purpose of this article was to study the enablement concept through a concept analysis in the health care context to identify: (1) its attributes and (2) its antecedents and consequents. A concept analysis was performed according to the method of Rodgers. The literature was reviewed from 1980 to June 2008, using search strategies adapted to the databases Cinahl, Medline, Embase, PsycInfo and Social Works Abstract, and hand searching. All articles contributing to a deeper understanding of the concept were included. The analysis was carried out according to a thematic analysis procedure, as described by Miles & Huberman. The search identified 1305 citations. After in-depth assessment of 148 potentially eligible citations, 61 articles were included in the review. Five articles were added with hand searching. Sixty-seven per cent of these articles were related to nursing. The attributes of the enablement concept included: contribution to the therapeutic relationship; consideration of the person as a whole; facilitation of learning; valorization of the person's strengths; implication and support to decision making; and broadening of the possibilities. These attributes could be used as a basis for other studies on enablement. Conceptual and empirical work is still needed to better position this concept among others such as patient-centred care, shared decision making and patient's participation. © 2010 Blackwell Publishing Ltd.

Hand hygiene among healthcare workers: A qualitative meta summary using the GRADE-CERQual process

PubMed Central

Chatfield, Sheryl L.; DeBois, Kristen; Nolan, Rachael; Crawford, Hannah; Hallam, Jeffrey S.

2016-01-01

Background: Hand hygiene is considered an effective and potentially modifiable infection control behaviour among healthcare workers (HCW). Several meta-studies have been published that compare quantitatively expressed findings, but limited efforts have been made to synthesise qualitative research. Objectives: This paper provides the first report of integrated findings from qualitative research reports on hand hygiene compliance among HCW worldwide that employs the GRADE-CERQual process of quality assessment. Methods: We conducted database searches and identified 36 reports in which authors conducted qualitative or mixed methods research on hand hygiene compliance among HCW. We used Dedoose analysis software to facilitate extraction of relevant excerpts. We applied the GRADE-CERQual process to describe relative confidence as high, moderate or low for nine aggregate findings. Findings: Highest confidence findings included that HCW believe they have access to adequate training, and that management and resource support are sometimes lacking. Individual, subjective criteria also influence hand hygiene. Discussion: These results suggest the need for further investigation into healthcare cultures that are perceived as supportive for infection control. Surveillance processes have potential, especially if information is perceived by HCW as timely and relevant. PMID:28989515

Health-care professionals' knowledge, attitudes and behaviours relating to patient capacity to consent to treatment: an integrative review.

PubMed

Lamont, Scott; Jeon, Yun-Hee; Chiarella, Mary

2013-09-01

This integrative review aims to provide a synthesis of research findings of health-care professionals' knowledge, attitudes and behaviours relating to patient capacity to consent to or refuse treatment within the general hospital setting. Search strategies included relevant health databases, hand searching of key journals, 'snowballing' and expert recommendations. The review identified various knowledge gaps and attitudinal dispositions of health-care professionals, which influence their behaviours and decision-making in relation to capacity to consent processes. The findings suggest that there is tension between legal, ethical and professional standards relating to the assessment of capacity and consent within health care. Legislation and policy guidance concerning capacity assessment processes are lacking, and this may contribute to inconsistencies in practice.

In search of the autologous clip: a case for experimental standardization.

PubMed

Krugman, Kimberly A; Martin, Kimberly E; Cosgriff, Ned; Slakey, Douglas P

2011-10-01

In an effort to enable faster and, at times, more challenging surgeries without compromising patient or physician safety, medical device manufacturers have created myriad solutions to vascular ligation through the development of novel tools. The speed of development, FDA approval, and dissemination of these devices into the hands of surgeons often outpaces the ability of investigators to critically evaluate comparative effectiveness of these devices. The Medline database was searched for energy-based vessel ligation devices. To remove any perception bias against non-Covidien instruments, critical review was applied only to the devices manufactured by our company. We report on the variability present in published results and offer vital metrics for future studies. Standardized testing and reporting for measures of safety and efficacy of these surgical instruments awaits definition from a consensus group.

Analysis of human serum phosphopeptidome by a focused database searching strategy.

PubMed

Zhu, Jun; Wang, Fangjun; Cheng, Kai; Song, Chunxia; Qin, Hongqiang; Hu, Lianghai; Figeys, Daniel; Ye, Mingliang; Zou, Hanfa

2013-01-14

As human serum is an important source for early diagnosis of many serious diseases, analysis of serum proteome and peptidome has been extensively performed. However, the serum phosphopeptidome was less explored probably because the effective method for database searching is lacking. Conventional database searching strategy always uses the whole proteome database, which is very time-consuming for phosphopeptidome search due to the huge searching space resulted from the high redundancy of the database and the setting of dynamic modifications during searching. In this work, a focused database searching strategy using an in-house collected human serum pro-peptidome target/decoy database (HuSPep) was established. It was found that the searching time was significantly decreased without compromising the identification sensitivity. By combining size-selective Ti (IV)-MCM-41 enrichment, RP-RP off-line separation, and complementary CID and ETD fragmentation with the new searching strategy, 143 unique endogenous phosphopeptides and 133 phosphorylation sites (109 novel sites) were identified from human serum with high reliability. Copyright © 2012 Elsevier B.V. All rights reserved.

Best practices to prevent transmission and control outbreaks of hand, foot, and mouth disease in childcare facilities: a systematic review.

PubMed

Chan, J Hy; Law, C K; Hamblion, E; Fung, H; Rudge, J

2017-04-01

Hand, foot, and mouth disease continues to cause seasonal epidemics in the Asia-Pacific Region. Since the current Enterovirus 71 vaccines do not provide cross-protection for all Enterovirus species that cause hand, foot, and mouth disease, there is an urgent need to identify appropriate detection tools and best practice to prevent its transmission and to effectively control its outbreaks. This systematic review aimed to identify characteristics of outbreak and assess the impact and effectiveness of detection tools and public health preventive measures to interrupt transmission. The findings will be used to recommend policy on the most effective responses and interventions in Hong Kong to effectively minimise and contain the spread of the disease within childcare facilities. We searched the following databases for primary studies written in Chinese or English: MEDLINE, EMBASE, Global Health, WHO Western Pacific Region Index Medicus database, China National Knowledge Infrastructure Databases, and Chinese Scientific Journals Database. Studies conducted during or retrospective to outbreaks of hand, foot, and mouth disease caused by Enterovirus 71 from 1980 to 2012 within childcare facilities and with a study population of 0 to 6 years old were included. Sixteen studies conducted on outbreaks in China showed that hand, foot, and mouth disease spread rapidly within the facility, with an outbreak length of 4 to 46 days, especially in those with delayed notification (after 24 hours) of clustered outbreak (with five or more cases discovered within the facility) to the local Center for Disease Control and Prevention and delayed implementation of a control response. The number of classes affected ranged from 1 to 13, and the attack rate for children ranged from 0.97% to 28.18%. Communication between key stakeholders about outbreak confirmation, risk assessment, and surveillance should be improved. Effective communication facilitates timely notification (within 24 hours) of clustered outbreaks to a local Center for Disease Control and Prevention. Timely implementation of a control response is effective in minimising incidence and length of an outbreak in childcare facilities. The government should provide incentives for childcare facilities to train infection control specialists who can serve as the first contact, knowledge, and communication points, as well as facilitate exchange of information and provision of support across stakeholders during a communicable disease epidemic.

A Critical Review of Search Strategies Used in Recent Systematic Reviews Published in Selected Prosthodontic and Implant-Related Journals: Are Systematic Reviews Actually Systematic?

PubMed

Layton, Danielle

The aim of this study was to outline how search strategies can be systematic, to examine how the searches in recent systematic reviews in prosthodontic and implant-related journals were structured, and to determine whether the search strategies used in those articles were systematic. A total of 103 articles published as systematic reviews and indexed in Medline between January 2013 and May 2016 were identified from eight prosthodontic and implant journals and reviewed. The search strategies were considered systematic when they met the following criteria: (1) more than one electronic database was searched, (2) more than one searcher was clearly involved, (3) both text words and indexing terms were clearly included in the search strategy, (4) a hand search of selected journals or reference lists was undertaken, (5) gray research was specifically sought, and (6) the articles were published in English and at least one other language. The data were tallied and qualitatively assessed. The majority of articles reported on implants (54%), followed by tooth-supported fixed prosthodontics (13%). A total of 23 different electronic resources were consulted, including Medline (by 100% of articles), the Cochrane Library (52%), and Embase (37%). The majority consulted more than one electronic resource (71%), clearly included more than one searcher (73%), and employed a hand search of either selected journals or reference lists (86%). Less than half used both text words and indexing terms to identify articles (42%), while 15% actively sought gray research. Articles published in languages other than English were considered in 63 reviews, but only 14 had no language restrictions. Of the 103 articles, 5 completed search strategies that met all 6 criteria, and a further 12 met 5 criteria. Two articles did not fulfill any of the criteria. More than 95% of recent prosthodontic and implant review articles published in the selected journals failed to use search strategies that were systematic, and this undermines the conclusions. Many resources are available to help investigators design search strategies for systematic reviews that minimize the risk of omitting important data, including the simple criteria presented in this paper.

Conservative physical therapy management for the treatment of cervicogenic headache: a systematic review.

PubMed

Racicki, Stephanie; Gerwin, Sarah; Diclaudio, Stacy; Reinmann, Samuel; Donaldson, Megan

2013-05-01

The purpose of this systematic review was to assess the effectiveness of conservative physical therapy management of cervicogenic headache (CGH). CGH affects 22-25% of the adult population with females being four times more affected than men. CGHs are thought to arise from musculoskeletal impairments in the neck with symptoms most commonly consisting of suboccipital neck pain, dizziness, and lightheadedness. Currently, both invasive and non-invasive techniques are available to address these symptoms; however, the efficacy of non-invasive treatment techniques has yet to be established. Computerized searches of CINAHL, ProQuest, PubMed, MEDLINE, and SportDiscus, were performed to obtain a qualitative analysis of the literature. Inclusion criteria were: randomized controlled trial design, population diagnosed with CGH using the International Headache Society classification, at least one baseline measurement and one outcomes measure, and assessment of a conservative technique. Physiotherapy evidence-based database scale was utilized for quality assessment. One computerized database search and two hand searches yielded six articles. Of the six included randomized controlled trials, all were considered to be of 'good quality' utilizing the physiotherapy evidence-based database scale. The interventions utilized were: therapist-driven cervical manipulation and mobilization, self-applied cervical mobilization, cervico-scapular strengthening, and therapist-driven cervical and thoracic manipulation. With the exception of one study, all reported reduction in pain and disability, as well as improvement in function. Calculated effect sizes allowed comparison of intervention groups between studies. A combination of therapist-driven cervical manipulation and mobilization with cervico-scapular strengthening was most effective for decreasing pain outcomes in those with CGH.

The effectiveness of dopamine agonists for treatment of neuropsychiatric symptoms post brain injury and stroke.

PubMed

Sami, Musa Basseer; Faruqui, Rafey

2015-12-01

Traumatic brain injury and stroke are among the leading causes of neurological disability worldwide. Although dopaminergic agents have long been associated with improvement of neuropsychiatric outcomes, to date much of the evidence to date has been in case reports and case series or open label trials. We undertook a systematic review of double-blinded randomised controlled trials (RCT) to determine the effect of dopaminergic agents on pre-defined outcomes of (a) apathy; (b) psychomotor retardation; (c) behavioural management and (d) cognitive function. Databases searched were: Medline, EMBASE, and PsychInfo for human studies. The Cochrane Clinical Trials Database and the TRIP Medical database were also searched. All identified studies, were further hand-searched. We identified six studies providing data on 227 participants, 150 of whom received dopaminergic therapy. Trials were compromised by cross-over design, inadequate wash out period, small numbers and heterogeneous outcome measures. However one good quality RCT demonstrates the efficacy of amantadine in behavioural management. One further RCT shows methylphenidate-levodopa is efficacious for mood post-stroke. One study shows rotigotine to improve hemi-inattention caused by prefrontal damage. Our systematic review demonstrates an evolving evidence base to suggest some benefits in agitation and aggression, mood and attentional deficits. However, there are key limitations of the studies undertaken to date involving small numbers of participants, heterogeneous outcome measures, and variable study designs. There is a need for on-going large prospective double-blind RCTs in these medications using standardised criteria and outcomes to fully understand their effectiveness in this patient group.

Mixed methods systematic review exploring mentorship outcomes in nursing academia.

PubMed

Nowell, Lorelli; Norris, Jill M; Mrklas, Kelly; White, Deborah E

2017-03-01

The aim of this study was to report on a mixed methods systematic review that critically examines the evidence for mentorship in nursing academia. Nursing education institutions globally have issued calls for mentorship. There is emerging evidence to support the value of mentorship in other disciplines, but the extant state of the evidence in nursing academia is not known. A comprehensive review of the evidence is required. A mixed methods systematic review. Five databases (MEDLINE, CINAHL, EMBASE, ERIC, PsycINFO) were searched using an a priori search strategy from inception to 2 November 2015 to identify quantitative, qualitative and mixed methods studies. Grey literature searches were also conducted in electronic databases (ProQuest Dissertations and Theses, Index to Theses) and mentorship conference proceedings and by hand searching the reference lists of eligible studies. Study quality was assessed prior to inclusion using standardized critical appraisal instruments from the Joanna Briggs Institute. A convergent qualitative synthesis design was used where results from qualitative, quantitative and mixed methods studies were transformed into qualitative findings. Mentorship outcomes were mapped to a theory-informed framework. Thirty-four studies were included in this review, from the 3001 records initially retrieved. In general, mentorship had a positive impact on behavioural, career, attitudinal, relational and motivational outcomes; however, the methodological quality of studies was weak. This review can inform the objectives of mentorship interventions and contribute to a more rigorous approach to studies that assess mentorship outcomes. © 2016 John Wiley & Sons Ltd.

A systematic review of peer mentoring interventions for people with traumatic brain injury.

PubMed

Morris, Richard Pg; Fletcher-Smith, Joanna C; Radford, Kathryn A

2017-08-01

This systematic review sought evidence concerning the effectiveness of peer mentoring for people with traumatic brain injury. Fourteen electronic databases were searched, including PsycINFO, MEDLINE, CINAHL, EMBASE and the Cochrane Library, from inception to September 21 2016. Ten grey literature databases, PROSPERO, two trials registers, reference lists and author citations were also searched. Studies which employed a model of one-to-one peer mentoring between traumatic brain injury survivors were included. Two reviewers independently screened all titles and abstracts before screening full texts of shortlisted studies. A third reviewer resolved disagreements. Two reviewers independently extracted data and assessed studies for quality and risk of bias. The search returned 753 records, including one identified through hand searching. 495 records remained after removal of duplicates and 459 were excluded after screening. Full texts were assessed for the remaining 36 studies and six met the inclusion criteria. All were conducted in the United States between 1996 and 2012 and employed a variety of designs including two randomised controlled trials. A total of 288 people with traumatic brain injury participated in the studies. No significant improvements in social activity level or social network size were found, but significant improvements were shown in areas including behavioural control, mood, coping and quality of life. There is limited evidence for the effectiveness of peer mentoring after traumatic brain injury. The available evidence comes from small-scale studies, of variable quality, without detailed information on the content of sessions or the 'active ingredient' of the interventions.

Effect of caffeine on vestibular evoked myogenic potential: a systematic review with meta-analysis.

PubMed

Souza, Maria Eduarda Di Cavalcanti Alves de; Costa, Klinger Vagner Teixeira da; Menezes, Pedro de Lemos

2017-12-24

Caffeine can be considered the most consumed drug by adults worldwide, and can be found in several foods, such as chocolate, coffee, tea, soda and others. Overall, caffeine in moderate doses, results in increased physical and intellectual productivity, increases the capacity of concentration and reduces the time of reaction to sensory stimuli. On the other hand, high doses can cause noticeable signs of mental confusion and error induction in intellectual tasks, anxiety, restlessness, muscle tremors, tachycardia, labyrinthine changes, and tinnitus. Considering that the vestibular evoked myogenic potential is a clinical test that evaluates the muscular response of high intensity auditory stimulation, the present systematic review aimed to analyze the effects of caffeine on vestibular evoked myogenic potential. This study consisted of the search of the following databases: MEDLINE, CENTRAL, ScienceDirect, Scopus, Web of Science, LILACS, SciELO and ClinicalTrials.gov. Additionally, the gray literature was also searched. The search strategy included terms related to intervention (caffeine or coffee consumption) and the primary outcome (vestibular evoked myogenic potential). Based on the 253 potentially relevant articles identified through the database search, only two full-text publications were retrieved for further evaluation, which were maintained for qualitative analysis. Analyzing the articles found, caffeine has no effect on vestibular evoked myogenic potential in normal individuals. Copyright © 2017 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

Economic evaluation of manual therapy for musculoskeletal diseases: a protocol for a systematic review and narrative synthesis of evidence.

PubMed

Kim, Chang-Gon; Mun, Su-Jeong; Kim, Ka-Na; Shin, Byung-Cheul; Kim, Nam-Kwen; Lee, Dong-Hyo; Lee, Jung-Han

2016-05-13

Manual therapy is the non-surgical conservative management of musculoskeletal disorders using the practitioner's hands on the patient's body for diagnosing and treating disease. The aim of this study is to systematically review trial-based economic evaluations of manual therapy relative to other interventions used for the management of musculoskeletal diseases. Randomised clinical trials (RCTs) on the economic evaluation of manual therapy for musculoskeletal diseases will be included in the review. The following databases will be searched from their inception: Medline, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), Cumulative Index to Nursing and Allied Health Literature (CINAHL), Econlit, Mantis, Index to Chiropractic Literature, Science Citation Index, Social Science Citation Index, Allied and Complementary Medicine Database (AMED), Cochrane Database of Systematic Reviews (CDSR), National Health Service Database of Abstracts of Reviews of Effects (NHS DARE), National Health Service Health Technology Assessment Database (NHS HTA), National Health Service Economic Evaluation Database (NHS EED), CENTRAL, five Korean medical databases (Oriental Medicine Advanced Searching Integrated System (OASIS), Research Information Service System (RISS), DBPIA, Korean Traditional Knowledge Portal (KTKP) and KoreaMed) and three Chinese databases (China National Knowledge Infrastructure (CNKI), VIP and Wanfang). The evidence for the cost-effectiveness, cost-utility and cost-benefit of manual therapy for musculoskeletal diseases will be assessed as the primary outcome. Health-related quality of life and adverse effects will be assessed as secondary outcomes. We will critically appraise the included studies using the Cochrane risk of bias tool and the Drummond checklist. Results will be summarised using Slavin's qualitative best-evidence synthesis approach. The results of the study will be disseminated via a peer-reviewed journal and/or conference presentations. PROSPERO CRD42015026757. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Efficacy of Instant Hand Sanitizers against Foodborne Pathogens Compared with Hand Washing with Soap and Water in Food Preparation Settings: A Systematic Review.

PubMed

Foddai, Antonio C G; Grant, Irene R; Dean, Moira

2016-06-01

Hands can be a vector for transmitting pathogenic microorganisms to foodstuffs and drinks, and to the mouths of susceptible hosts. Hand washing is the primary barrier to prevent transmission of enteric pathogens via cross-contamination from infected persons. Conventional hand washing involves the use of water, soap, and friction to remove dirt and microorganisms. The availability of hand sanitizing products for use when water and soap are unavailable has increased in recent years. The aim of this systematic review was to collate scientific information on the efficacy of hand sanitizers compared with washing hands with soap and water for the removal of foodborne pathogens from the hands of food handlers. An extensive literature search was carried out using three electronic databases: Web of Science, Scopus, and PubMed. Twenty-eight scientific publications were ultimately included in the review. Analysis of this literature revealed various limitations in the scientific information owing to the absence of a standardized protocol for evaluating the efficacy of hand products and variation in experimental conditions. However, despite conflicting results, scientific evidence seems to support the historical skepticism about the use of waterless hand sanitizers in food preparation settings. Water and soap appear to be more effective than waterless products for removal of soil and microorganisms from hands. Alcohol-based products achieve rapid and effective inactivation of various bacteria, but their efficacy is generally lower against nonenveloped viruses. The presence of food debris significantly affects the microbial inactivation rate of hand sanitizers.

Interventions to improve hand hygiene compliance in patient care.

PubMed

Gould, Dinah J; Moralejo, Donna; Drey, Nicholas; Chudleigh, Jane H

2010-09-08

Health care-associated infection is a major cause of morbidity and mortality. Hand hygiene is regarded as an effective preventive measure. To update the review done in 2007, to assess the short and longer-term success of strategies to improve hand hygiene compliance and to determine whether a sustained increase in hand hygiene compliance can reduce rates of health care-associated infection. We conducted electronic searches of: the Cochrane Central Register of Controlled Trials; the Cochrane Effective Practice and Organisation of Care Group specialised register of trials; MEDLINE; PubMed; EMBASE; CINAHL; and the BNI. Originally searched to July 2006, for the update databases were searched from August 2006 until November 2009. Randomised controlled trials, controlled clinical trials, controlled before and after studies, and interrupted time series analyses meeting explicit entry and quality criteria used by the Cochrane Effective Practice and Organisation of Care Group were eligible for inclusion. Studies reporting indicators of hand hygiene compliance and proxy indicators such as product use were considered. Self-reported data were not considered a valid measure of compliance. Studies to promote hand hygiene compliance as part of a care bundle approach were included, providing data relating specifically to hand hygiene were presented separately. Studies were excluded if hand hygiene was assessed in simulations, non-clinical settings or the operating theatre setting. Two reviewers independently extracted data and assessed data quality. Four studies met the criteria for the review: two from the original review and two from the update. Two studies evaluated simple education initiatives, one using a randomized clinical trial design and the other a controlled before and after design. Both measured hand hygiene compliance by direct observation. The other two studies were both interrupted times series studies. One study presented three separate interventions within the same paper: simple substitutions of product and two multifaceted campaigns, one of which included involving practitioners in making decisions about choice of hand hygiene products and the components of the hand hygiene program. The other study also presented two separate multifaceted campaigns, one of which involved application of social marketing theory. In these two studies follow-up data collection continued beyond twelve months, and a proxy measure of hand hygiene compliance (product use) was recorded. Microbiological data were recorded in one study. Hand hygiene compliance increased for one of the studies where it was measured by direct observation, but the results from the other study were not conclusive. Product use increased in the two studies in which it was reported, with inconsistent results reported for one initiative. MRSA incidence decreased in the one study reporting microbiological data. The quality of intervention studies intended to increase hand hygiene compliance remains disappointing. Although multifaceted campaigns with social marketing or staff involvement appear to have an effect, there is insufficient evidence to draw a firm conclusion. There remains an urgent need to undertake methodologically robust research to explore the effectiveness of soundly designed and implemented interventions to increase hand hygiene compliance.

EasyKSORD: A Platform of Keyword Search Over Relational Databases

NASA Astrophysics Data System (ADS)

Peng, Zhaohui; Li, Jing; Wang, Shan

Keyword Search Over Relational Databases (KSORD) enables casual users to use keyword queries (a set of keywords) to search relational databases just like searching the Web, without any knowledge of the database schema or any need of writing SQL queries. Based on our previous work, we design and implement a novel KSORD platform named EasyKSORD for users and system administrators to use and manage different KSORD systems in a novel and simple manner. EasyKSORD supports advanced queries, efficient data-graph-based search engines, multiform result presentations, and system logging and analysis. Through EasyKSORD, users can search relational databases easily and read search results conveniently, and system administrators can easily monitor and analyze the operations of KSORD and manage KSORD systems much better.

Family support for reducing morbidity and mortality in people with HIV/AIDS.

PubMed

Mohanan, Padma; Kamath, Asha

2009-07-08

Care and support play a critical role in assisting people who are HIV-positive to understand the need for prevention and to enable them to protect others. As the HIV/AIDS pandemic progresses and HIV-seropositive individuals contend with devastating illness, it seemed timely to inquire if they receive support from family members. It also was important to develop a normative idea of how much family support exists and from whom it emanates. To assess the effect of family support on morbidity, mortality, quality of life, and economics in families with at least one HIV-infected member, in developing countries. The following databases were searched:The Cochrane Central Register for Controlled Trials (CENTRAL), the Cochrane Database of Systematic Reviews, MEDLINE, AIDSLINE, CINAHL, Dissertation Abstracts International (DAI), EMBASE, BIOSIS, SCISEARCH, the Cochrane HIV/AIDS group specialized register, INDMED, Proquest, and various South Asian abstracting databases, will be included in the database list. The publication sites of the World Health Organization, the US Centers for Disease Control and Prevention, and other international research and non-governmental organizations. An extensive search strategy string was developed in consultation with the trial search coordinator of the HIV/AIDS Review Group. Numerous relevant keywords were included in the string to get an exhaustive electronic literature search. The search was not restricted by language. Articles from other languages were translated into English with the help of experts. A hand search was carried out in many journals and abstracts of the conference proceedings of national and international conferences related to AIDS (e.g. the International Conference on HIV/AIDS and STI in Africa [ICASA]). Efforts also were made to contact experts to identify unpublished research and trials still underway. Intervention studies. Randomized control trials (RCTs) and quasi-RCTs involving HIV-infected individuals with family support in developing countries. We independently screened the results of the search to select potentially relevant studies and to retrieve the full articles. We independently applied the inclusion criteria to the potentially relevant studies. No studies were identified that fulfilled the selection criteria. We were unable to find any trials of family support in reducing the morbidity and mortality in HIV-infected persons in developing countries. There is insufficient evidence to bring out the effect of family support in reducing the morbidity and mortality of HIV-infected persons in developing countries. This review has highlighted the dearth of high-quality quantitative research about family support. There is a clear need for rigorous studies of the clinical effects of family support on people with HIV in developing countries.

Using SQL Databases for Sequence Similarity Searching and Analysis.

PubMed

Pearson, William R; Mackey, Aaron J

2017-09-13

Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Find a Hand Surgeon

MedlinePlus

... you agree to the user agreement and disclaimer . Search By Location Search By Doctor Search Results Map Enter a location ... by American Society for Surgery of the Hand × Search Tips Tip 1: Start with the basics like " ...

Sensory re-education after nerve injury of the upper limb: a systematic review.

PubMed

Oud, Tanja; Beelen, Anita; Eijffinger, Elianne; Nollet, Frans

2007-06-01

To systematically review the available evidence for the effectiveness of sensory re-education to improve the sensibility of the hand in patients with a peripheral nerve injury of the upper limb. Studies were identified by an electronic search in the databases MEDLINE, Cumulative Index to Nursing & Allied Health Literature (CINAHL), EMBASE, the Cochrane Library, the Physiotherapy Evidence Database (PEDro), and the database of the Dutch National Institute of Allied Health Professions (Doconline) and by screening the reference lists of relevant articles. Two reviewers selected studies that met the following inclusion criteria: all designs except case reports, adults with impaired sensibility of the hand due to a peripheral nerve injury of the upper limb, and sensibility and functional sensibility as outcome measures. The methodological quality of the included studies was independently assessed by two reviewers. A best-evidence synthesis was performed, based on design, methodological quality and significant findings on outcome measures. Seven studies, with sample sizes ranging from 11 to 49, were included in the systematic review and appraised for content. Five of these studies were of poor methodological quality. One uncontrolled study (N = 1 3 ) was considered to be of sufficient methodological quality, and one randomized controlled trial (N = 49) was of high methodological quality. Best-evidence synthesis showed that there is limited evidence for the effectiveness of sensory re-education, provided by a statistically significant improvement in sensibility found in one high-quality randomized controlled trial. There is a need for further well-defined clinical trials to assess the effectiveness of sensory re-education of patients with impaired sensibility of the hand due to a peripheral nerve injury.

Identifying Lesbian, Gay, Bisexual, and Transgender Search Terminology: A Systematic Review of Health Systematic Reviews

PubMed Central

Lee, Joseph G. L.; Ylioja, Thomas; Lackey, Mellanye

2016-01-01

Research on the health of lesbian, gay, bisexual, and transgender (LGBT) populations can provide important information to address existing health inequalities. Finding existing research in LGBT health can prove challenging due to the plethora of terminology used. We sought to describe existing search strategies and to identify more comprehensive LGBT search terminology. We iteratively created a search string to identify systematic reviews and meta-analyses about LGBT health and implemented it in Embase, PubMed/MEDLINE, and PsycINFO databases on May 28–29, 2015. We hand-searched the journal LGBT Health. Inclusion criteria were: systematic reviews and meta-analyses that addressed LGBT health, used systematic searching, and used independent coders for inclusion. The published search terminology in each record and search strings provided by authors on request were cross-referenced with our original search to identify additional terminology. Our search process identified 19 systematic reviews meeting inclusion criteria. The number of search terms used to identify LGBT-related records ranged from 1 to 31. From the included studies, we identified 46 new search terms related to LGBT health. We removed five search terms as inappropriate and added five search terms used in the field. The resulting search string included 82 terms. There is room to improve the quality of searching and reporting in LGBT health systematic reviews. Future work should attempt to enhance the positive predictive value of LGBT health searches. Our findings can assist LGBT health reviewers in capturing the diversity of LGBT terminology when searching. PMID:27219460

In Vivo and In Vitro Effectiveness of Rotary Nickel-Titanium vs Manual Stainless Steel Instruments for Root Canal Therapy: Systematic Review and Meta-analysis.

PubMed

Del Fabbro, Massimo; Afrashtehfar, Kelvin Ian; Corbella, Stefano; El-Kabbaney, Ahmed; Perondi, Isabella; Taschieri, Silvio

2018-03-01

This systematic review evaluated the effectiveness of nickel-titanium (NiTi) rotary files compared to stainless-steel (SST) hand files. An electronic search was performed on Medline, EMBASE, CENTRAL and Scopus databases up to February 2016. An additional hand searching was performed in 13 journals. The studies were classified according to study type and the outcome variables. Two reviewers independently applied eligibility criteria, extracted data, and three reviewers independently assessed the quality of the evidence of each included study according to The Cochrane Collaboration's procedures. A meta-analysis was performed whenever it was possible. The electronic and hand search strategies yielded 1155 references of studies after removal of duplicates. Four clinical studies (two prospective and two retrospective studies) and 18 in vitro studies (on extracted teeth) were included for the qualitative synthesis after full-text evaluation of the eligible studies. The overall level of methodological quality of the studies included can be considered inadequate. Only one clinical study was judged at low risk of bias, whereas most non-clinical studies had a low risk of bias. Three meta-analyses, based on a very limited number of studies, could be performed. Each meta-analysis contained two studies. Of these, one meta-analysis was based on clinical studies. The results of this systematic review suggested that NiTi rotary instruments were associated with lower canal transportation and apical extrusion when compared to SST hand files, whereas both groups had similar outcomes in terms of success of therapy, amount of residual bacteria, and cleansing ability after treatment. However, due to the limited evidence available, these results should be interpreted with caution. Consequently, more randomized control trials using standardized protocols are needed in order to provide more solid recommendations. Copyright © 2017 Elsevier Inc. All rights reserved.

Native Health Research Database

MedlinePlus

... Indian Health Board) Welcome to the Native Health Database. Please enter your search terms. Basic Search Advanced ... To learn more about searching the Native Health Database, click here. Tutorial Video The NHD has made ...

Library Instruction and Online Database Searching.

ERIC Educational Resources Information Center

Mercado, Heidi

1999-01-01

Reviews changes in online database searching in academic libraries. Topics include librarians conducting all searches; the advent of end-user searching and the need for user instruction; compact disk technology; online public catalogs; the Internet; full text databases; electronic information literacy; user education and the remote library user;…

HOWDY: an integrated database system for human genome research

PubMed Central

Hirakawa, Mika

2002-01-01

HOWDY is an integrated database system for accessing and analyzing human genomic information (http://www-alis.tokyo.jst.go.jp/HOWDY/). HOWDY stores information about relationships between genetic objects and the data extracted from a number of databases. HOWDY consists of an Internet accessible user interface that allows thorough searching of the human genomic databases using the gene symbols and their aliases. It also permits flexible editing of the sequence data. The database can be searched using simple words and the search can be restricted to a specific cytogenetic location. Linear maps displaying markers and genes on contig sequences are available, from which an object can be chosen. Any search starting point identifies all the information matching the query. HOWDY provides a convenient search environment of human genomic data for scientists unsure which database is most appropriate for their search. PMID:11752279

Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data.

PubMed

Kumar, Dhirendra; Yadav, Amit Kumar; Dash, Debasis

2017-01-01

Database searching is the preferred method for protein identification from digital spectra of mass to charge ratios (m/z) detected for protein samples through mass spectrometers. The search database is one of the major influencing factors in discovering proteins present in the sample and thus in deriving biological conclusions. In most cases the choice of search database is arbitrary. Here we describe common search databases used in proteomic studies and their impact on final list of identified proteins. We also elaborate upon factors like composition and size of the search database that can influence the protein identification process. In conclusion, we suggest that choice of the database depends on the type of inferences to be derived from proteomics data. However, making additional efforts to build a compact and concise database for a targeted question should generally be rewarding in achieving confident protein identifications.

What else should we know about experiencing COPD? A narrative review in search of patients' psychological burden alleviation.

PubMed

Rzadkiewicz, Marta; Bråtas, Ola; Espnes, Geir Arild

2016-01-01

The present paper is a narrative review focusing on the psychological impact, identification of protective factors, and interventions minimizing the psychological burdens of chronic obstructive pulmonary disease (COPD). The research reviews studies on neurocognitive functions, personality, emotional problems, and health-related quality of life. This is done with regard to resources as well as activities enabling or enhancing a patient's adaptation. PubMed and PsychArticles databases were searched for relevant medical (eg, CODP, emphysema), psychopathology (eg, depression), and psychological (eg, personality) keywords, followed by hand search. After application of the inclusion and exclusion criteria, the search resulted in 82 articles and book chapters. The choice was based on evidence accepted by evidence-based medicine, although at different levels of strength. Psychological experiencing of COPD appears to be very unequally represented with scientific research on emotional problems and functioning decrease significantly outnumbering those addressing resources or effective interventions. As our initial literature search called for an urgent need for further exploration, we have carefully pointed out numerous areas where the knowledge on how to protect or restore psychological well-being among COPD patients should be broadened.

Towards computational improvement of DNA database indexing and short DNA query searching.

PubMed

Stojanov, Done; Koceski, Sašo; Mileva, Aleksandra; Koceska, Nataša; Bande, Cveta Martinovska

2014-09-03

In order to facilitate and speed up the search of massive DNA databases, the database is indexed at the beginning, employing a mapping function. By searching through the indexed data structure, exact query hits can be identified. If the database is searched against an annotated DNA query, such as a known promoter consensus sequence, then the starting locations and the number of potential genes can be determined. This is particularly relevant if unannotated DNA sequences have to be functionally annotated. However, indexing a massive DNA database and searching an indexed data structure with millions of entries is a time-demanding process. In this paper, we propose a fast DNA database indexing and searching approach, identifying all query hits in the database, without having to examine all entries in the indexed data structure, limiting the maximum length of a query that can be searched against the database. By applying the proposed indexing equation, the whole human genome could be indexed in 10 hours on a personal computer, under the assumption that there is enough RAM to store the indexed data structure. Analysing the methodology proposed by Reneker, we observed that hits at starting positions [Formula: see text] are not reported, if the database is searched against a query shorter than [Formula: see text] nucleotides, such that [Formula: see text] is the length of the DNA database words being mapped and [Formula: see text] is the length of the query. A solution of this drawback is also presented.

Heart Failure in Patients with Chronic Kidney Disease: A Systematic Integrative Review

PubMed Central

Segall, Liviu; Nistor, Ionut; Covic, Adrian

2014-01-01

Introduction. Heart failure (HF) is highly prevalent in patients with chronic kidney disease (CKD) and end-stage renal disease (ESRD) and is strongly associated with mortality in these patients. However, the treatment of HF in this population is largely unclear. Study Design. We conducted a systematic integrative review of the literature to assess the current evidence of HF treatment in CKD patients, searching electronic databases in April 2014. Synthesis used narrative methods. Setting and Population. We focused on adults with a primary diagnosis of CKD and HF. Selection Criteria for Studies. We included studies of any design, quantitative or qualitative. Interventions. HF treatment was defined as any formal means taken to improve the symptoms of HF and/or the heart structure and function abnormalities. Outcomes. Measures of all kinds were considered of interest. Results. Of 1,439 results returned by database searches, 79 articles met inclusion criteria. A further 23 relevant articles were identified by hand searching. Conclusions. Control of fluid overload, the use of beta-blockers and angiotensin-converting enzyme inhibitors or angiotensin receptor blockers, and optimization of dialysis appear to be the most important methods to treat HF in CKD and ESRD patients. Aldosterone antagonists and digitalis glycosides may additionally be considered; however, their use is associated with significant risks. The role of anemia correction, control of CKD-mineral and bone disorder, and cardiac resynchronization therapy are also discussed. PMID:24959595

FTree query construction for virtual screening: a statistical analysis.

PubMed

Gerlach, Christof; Broughton, Howard; Zaliani, Andrea

2008-02-01

FTrees (FT) is a known chemoinformatic tool able to condense molecular descriptions into a graph object and to search for actives in large databases using graph similarity. The query graph is classically derived from a known active molecule, or a set of actives, for which a similar compound has to be found. Recently, FT similarity has been extended to fragment space, widening its capabilities. If a user were able to build a knowledge-based FT query from information other than a known active structure, the similarity search could be combined with other, normally separate, fields like de-novo design or pharmacophore searches. With this aim in mind, we performed a comprehensive analysis of several databases in terms of FT description and provide a basic statistical analysis of the FT spaces so far at hand. Vendors' catalogue collections and MDDR as a source of potential or known "actives", respectively, have been used. With the results reported herein, a set of ranges, mean values and standard deviations for several query parameters are presented in order to set a reference guide for the users. Applications on how to use this information in FT query building are also provided, using a newly built 3D-pharmacophore from 57 5HT-1F agonists and a published one which was used for virtual screening for tRNA-guanine transglycosylase (TGT) inhibitors.

FTree query construction for virtual screening: a statistical analysis

NASA Astrophysics Data System (ADS)

Gerlach, Christof; Broughton, Howard; Zaliani, Andrea

2008-02-01

FTrees (FT) is a known chemoinformatic tool able to condense molecular descriptions into a graph object and to search for actives in large databases using graph similarity. The query graph is classically derived from a known active molecule, or a set of actives, for which a similar compound has to be found. Recently, FT similarity has been extended to fragment space, widening its capabilities. If a user were able to build a knowledge-based FT query from information other than a known active structure, the similarity search could be combined with other, normally separate, fields like de-novo design or pharmacophore searches. With this aim in mind, we performed a comprehensive analysis of several databases in terms of FT description and provide a basic statistical analysis of the FT spaces so far at hand. Vendors' catalogue collections and MDDR as a source of potential or known "actives", respectively, have been used. With the results reported herein, a set of ranges, mean values and standard deviations for several query parameters are presented in order to set a reference guide for the users. Applications on how to use this information in FT query building are also provided, using a newly built 3D-pharmacophore from 57 5HT-1F agonists and a published one which was used for virtual screening for tRNA-guanine transglycosylase (TGT) inhibitors.

Rapid identification of anonymous subjects in large criminal databases: problems and solutions in IAFIS III/FBI subject searches

NASA Astrophysics Data System (ADS)

Kutzleb, C. D.

1997-02-01

The high incidence of recidivism (repeat offenders) in the criminal population makes the use of the IAFIS III/FBI criminal database an important tool in law enforcement. The problems and solutions employed by IAFIS III/FBI criminal subject searches are discussed for the following topics: (1) subject search selectivity and reliability; (2) the difficulty and limitations of identifying subjects whose anonymity may be a prime objective; (3) database size, search workload, and search response time; (4) techniques and advantages of normalizing the variability in an individual's name and identifying features into identifiable and discrete categories; and (5) the use of database demographics to estimate the likelihood of a match between a search subject and database subjects.

What is lost when searching only one literature database for articles relevant to injury prevention and safety promotion?

PubMed

Lawrence, D W

2008-12-01

To assess what is lost if only one literature database is searched for articles relevant to injury prevention and safety promotion (IPSP) topics. Serial textword (keyword, free-text) searches using multiple synonym terms for five key IPSP topics (bicycle-related brain injuries, ethanol-impaired driving, house fires, road rage, and suicidal behaviors among adolescents) were conducted in four of the bibliographic databases that are most used by IPSP professionals: EMBASE, MEDLINE, PsycINFO, and Web of Science. Through a systematic procedure, an inventory of articles on each topic in each database was conducted to identify the total unduplicated count of all articles on each topic, the number of articles unique to each database, and the articles available if only one database is searched. No single database included all of the relevant articles on any topic, and the database with the broadest coverage differed by topic. A search of only one literature database will return 16.7-81.5% (median 43.4%) of the available articles on any of five key IPSP topics. Each database contributed unique articles to the total bibliography for each topic. A literature search performed in only one database will, on average, lead to a loss of more than half of the available literature on a topic.

A Fast, Minimalist Search Tool for Remote Sensing Data

NASA Astrophysics Data System (ADS)

Lynnes, C. S.; Macharrie, P. G.; Elkins, M.; Joshi, T.; Fenichel, L. H.

2005-12-01

We present a tool that emphasizes speed and simplicity in searching remotely sensed Earth Science data. The tool, nicknamed "Mirador" (Spanish for a scenic overlook), provides only four freetext search form fields, for Keywords, Location, Data Start and Data Stop. This contrasts with many current Earth Science search tools that offer highly structured interfaces in order to ensure precise, non-zero results. The disadvantages of the structured approach lie in its complexity and resultant learning curve, as well as the time it takes to formulate and execute the search, thus discouraging iterative discovery. On the other hand, the success of the basic Google search interface shows that many users are willing to forgo high search precision if the search process is fast enough to enable rapid iteration. Therefore, we employ several methods to increase the speed of search formulation and execution. Search formulation is expedited by the minimalist search form, with only one required field. Also, a gazetteer enables the use of geographic terms as shorthand for latitude/longitude coordinates. The search execution is accelerated by initially presenting dataset results (returned from a Google Mini appliance) with an estimated number of "hits" for each dataset based on the user's space-time constraints. The more costly file-level search is executed against a PostGres database only when the user "drills down", and then covering only the fraction of the time period needed to return the next page of results. The simplicity of the search form makes the tool easy to learn and use, and the speed of the searches enables an iterative form of data discovery.

A Systematic Review of Unmet Information and Psychosocial Support Needs of Adults Diagnosed with Thyroid Cancer.

PubMed

Hyun, Yong Gyu; Alhashemi, Ahmad; Fazelzad, Rouhi; Goldberg, Alyse S; Goldstein, David P; Sawka, Anna M

2016-09-01

Patient education and psychosocial support to patients are important elements of comprehensive cancer care, but the needs of thyroid cancer survivors are not well understood. The published English-language quantitative literature on (i) unmet medical information and (ii) psychosocial support needs of thyroid cancer survivors was systematically reviewed. A librarian information specialist searched seven electronic databases and a hand search was conducted. Two reviewers independently screened citations from the electronic search and reviewed relevant full-text papers. There was consensus between reviewers on the included papers, and duplicate independent abstraction was performed. The results were summarized descriptively. A total of 1984 unique electronic citations were screened, and 51 full-text studies were reviewed (three from the hand search). Seven cross-sectional, single-arm, survey studies were included, containing data from 6215 thyroid cancer survivor respondents. The respective study sizes ranged from 57 to 2398 subjects. All of the studies had some methodological limitations. Unmet information needs were variable relating to the disease, diagnostic tests, treatments, and co-ordination of medical care. There were relatively high unmet information needs related to aftercare (especially long-term effects of the disease or its treatment and its management) and psychosocial concerns (including practical and financial matters). Psychosocial support needs were incompletely met. Patient information on complementary and alternative medicine was very limited. In conclusion, thyroid cancer survivors perceive many unmet information needs, and these needs extend to aftercare. Psychosocial information and supportive care needs may be insufficiently met in this population. More work is needed to improve knowledge translation and psychosocial support for thyroid cancer survivors.

Emotion skills training for medical students: a systematic review.

PubMed

Satterfield, Jason M; Hughes, Ellen

2007-10-01

To identify emotion skills training methods and outcomes using a systematic review of medical student curricula studies. We searched the English language literature listed in the PubMed, Educational Resources Information Center (ERIC), PsycINFO and Web of Science databases, from 1980 to the present, using a comprehensive list of emotion skills keywords and subsequent hand searches. A total of 828 articles were initially identified. A manual search yielded 161 articles on broadly defined emotion skills educational programmes for medical students. A more stringent review and hand search of reference lists yielded a final 26 articles that included 'other-directed' emotion skills (i.e. cognitive and behavioural skills intended to manage the emotions of others), a description of the training programme, and assessment data. Emotion skills courses varied by total number of contact hours (2-64 hours), session frequency (from 1 session per day to 1 session every 6 months), duration (2 weeks to 2 years), pedagogy, patients targeted and educational outcomes. Student evaluation data were positive. Fifteen of 26 studies used objective emotion skills measures. Only 6/26 studies included a control or comparison condition and 5/26 used a randomised, controlled trial (RCT) design. All 5 RCTs showed positive outcomes with modest improvements in emotion communication skills, empathy, use of emotion words, supportive behaviours and enriched patient understanding. The heterogeneity of emotion skills curricular studies makes direct comparisons difficult. However, all controlled trials showed positive outcomes, suggesting the importance and effectiveness of 'other-directed' emotion skills training. No specific recommendations about curricular amount and frequency, timing and pedagogy can be made.

Maxillofacial growth and speech outcome after one-stage or two-stage palatoplasty in unilateral cleft lip and palate. A systematic review.

PubMed

Reddy, Rajgopal R; Gosla Reddy, Srinivas; Vaidhyanathan, Anitha; Bergé, Stefaan J; Kuijpers-Jagtman, Anne Marie

2017-06-01

The number of surgical procedures to repair a cleft palate may play a role in the outcome for maxillofacial growth and speech. The aim of this systematic review was to investigate the relationship between the number of surgical procedures performed to repair the cleft palate and maxillofacial growth, speech and fistula formation in non-syndromic patients with unilateral cleft lip and palate. An electronic search was performed in PubMed/old MEDLINE, the Cochrane Library, EMBASE, Scopus and CINAHL databases for publications between 1960 and December 2015. Publications before 1950-journals of plastic and maxillofacial surgery-were hand searched. Additional hand searches were performed on studies mentioned in the reference lists of relevant articles. Search terms included unilateral, cleft lip and/or palate and palatoplasty. Two reviewers assessed eligibility for inclusion, extracted data, applied quality indicators and graded level of evidence. Twenty-six studies met the inclusion criteria. All were retrospective and non-randomized comparisons of one- and two-stage palatoplasty. The methodological quality of most of the studies was graded moderate to low. The outcomes concerned the comparison of one- and two-stage palatoplasty with respect to growth of the mandible, maxilla and cranial base, and speech and fistula formation. Due to the lack of high-quality studies there is no conclusive evidence of a relationship between one- or two-stage palatoplasty and facial growth, speech and fistula formation in patients with unilateral cleft lip and palate. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Comparison Study of Overlap among 21 Scientific Databases in Searching Pesticide Information.

ERIC Educational Resources Information Center

Meyer, Daniel E.; And Others

1983-01-01

Evaluates overlapping coverage of 21 scientific databases used in 10 online pesticide searches in an attempt to identify minimum number of databases needed to generate 90 percent of unique, relevant citations for given search. Comparison of searches combined under given pesticide usage (herbicide, fungicide, insecticide) is discussed. Nine…

Content based information retrieval in forensic image databases.

PubMed

Geradts, Zeno; Bijhold, Jurrien

2002-03-01

This paper gives an overview of the various available image databases and ways of searching these databases on image contents. The developments in research groups of searching in image databases is evaluated and compared with the forensic databases that exist. Forensic image databases of fingerprints, faces, shoeprints, handwriting, cartridge cases, drugs tablets, and tool marks are described. The developments in these fields appear to be valuable for forensic databases, especially that of the framework in MPEG-7, where the searching in image databases is standardized. In the future, the combination of the databases (also DNA-databases) and possibilities to combine these can result in stronger forensic evidence.

Sensory overload: A concept analysis.

PubMed

Scheydt, Stefan; Müller Staub, Maria; Frauenfelder, Fritz; Nielsen, Gunnar H; Behrens, Johann; Needham, Ian

2017-04-01

In the context of mental disorders sensory overload is a widely described phenomenon used in conjunction with psychiatric interventions such as removal from stimuli. However, the theoretical foundation of sensory overload as addressed in the literature can be described as insufficient and fragmentary. To date, the concept of sensory overload has not yet been sufficiently specified or analyzed. The aim of the study was to analyze the concept of sensory overload in mental health care. A literature search was undertaken using specific electronic databases, specific journals and websites, hand searches, specific library catalogues, and electronic publishing databases. Walker and Avant's method of concept analysis was used to analyze the sources included in the analysis. All aspects of the method of Walker and Avant were covered in this concept analysis. The conceptual understanding has become more focused, the defining attributes, influencing factors and consequences are described and empirical referents identified. The concept analysis is a first step in the development of a middle-range descriptive theory of sensory overload based on social scientific and stress-theoretical approaches. This specification may serve as a fundament for further research, for the development of a nursing diagnosis or for guidelines. © 2017 Australian College of Mental Health Nurses Inc.

Social marketing analysis of 20 [corrected] years of hand hygiene promotion.

PubMed

Mah, Manuel W; Tam, Yat Cho; Deshpande, Sameer

2008-03-01

To assess published hand hygiene behavioral interventions that employed a social marketing framework and to recommend improvements to future interventions. We performed a systematic literature review by searching the PubMed database and the Cumulative Index to Nursing and Allied Health Literature for published articles about hand hygiene behavioral interventions in healthcare facilities, schools, and community settings. Our analysis included articles that describe multifaceted interventions and evaluated them with predefined social marketing benchmark criteria. Of 53 interventions analyzed in this review, 16 (30.2%) employed primary formative audience research, 5 (9.4%) incorporated social or behavioral theories, 27 (50.9%) employed segmentation and targeting of the audience, 44 (83.0%) used components of the "marketing mix," 3 (5.7%) considered the influence of competing behaviors, 7 (13.2%) cultivated relationships with the target audience, and 15 (28.3%) provided simple behavioral messages. Thirty-five (66.0%) of the interventions demonstrated a significant improvement in performance, but only 21 (39.6%) were considered to have a strong evaluative design. The median duration of the interventions was 8.0 months. From a social marketing perspective, the promotion of hand hygiene could be improved in several ways. The effectiveness of social marketing in hand hygiene promotion should be tested in future interventions.

Searching for religion and mental health studies required health, social science, and grey literature databases.

PubMed

Wright, Judy M; Cottrell, David J; Mir, Ghazala

2014-07-01

To determine the optimal databases to search for studies of faith-sensitive interventions for treating depression. We examined 23 health, social science, religious, and grey literature databases searched for an evidence synthesis. Databases were prioritized by yield of (1) search results, (2) potentially relevant references identified during screening, (3) included references contained in the synthesis, and (4) included references that were available in the database. We assessed the impact of databases beyond MEDLINE, EMBASE, and PsycINFO by their ability to supply studies identifying new themes and issues. We identified pragmatic workload factors that influence database selection. PsycINFO was the best performing database within all priority lists. ArabPsyNet, CINAHL, Dissertations and Theses, EMBASE, Global Health, Health Management Information Consortium, MEDLINE, PsycINFO, and Sociological Abstracts were essential for our searches to retrieve the included references. Citation tracking activities and the personal library of one of the research teams made significant contributions of unique, relevant references. Religion studies databases (Am Theo Lib Assoc, FRANCIS) did not provide unique, relevant references. Literature searches for reviews and evidence syntheses of religion and health studies should include social science, grey literature, non-Western databases, personal libraries, and citation tracking activities. Copyright © 2014 Elsevier Inc. All rights reserved.

Molecule database framework: a framework for creating database applications with chemical structure search capability

PubMed Central

2013-01-01

Background Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Results Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes: • Support for multi-component compounds (mixtures) • Import and export of SD-files • Optional security (authorization) For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. Conclusions By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework. PMID:24325762

Molecule database framework: a framework for creating database applications with chemical structure search capability.

PubMed

Kiener, Joos

2013-12-11

Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework successfully abstracts chemical structure searches and SD-File import and export to simple method calls. The framework offers good search performance on a standard laptop without any database tuning. This is also due to the fact that chemical structure searches are paged and cached. Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

PubMed

Wang, Chunlin; Lefkowitz, Elliot J

2004-10-28

Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

PubMed Central

Wang, Chunlin; Lefkowitz, Elliot J

2004-01-01

Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Conclusions Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist. PMID:15511296

Large-scale feature searches of collections of medical imagery

NASA Astrophysics Data System (ADS)

Hedgcock, Marcus W.; Karshat, Walter B.; Levitt, Tod S.; Vosky, D. N.

1993-09-01

Large scale feature searches of accumulated collections of medical imagery are required for multiple purposes, including clinical studies, administrative planning, epidemiology, teaching, quality improvement, and research. To perform a feature search of large collections of medical imagery, one can either search text descriptors of the imagery in the collection (usually the interpretation), or (if the imagery is in digital format) the imagery itself. At our institution, text interpretations of medical imagery are all available in our VA Hospital Information System. These are downloaded daily into an off-line computer. The text descriptors of most medical imagery are usually formatted as free text, and so require a user friendly database search tool to make searches quick and easy for any user to design and execute. We are tailoring such a database search tool (Liveview), developed by one of the authors (Karshat). To further facilitate search construction, we are constructing (from our accumulated interpretation data) a dictionary of medical and radiological terms and synonyms. If the imagery database is digital, the imagery which the search discovers is easily retrieved from the computer archive. We describe our database search user interface, with examples, and compare the efficacy of computer assisted imagery searches from a clinical text database with manual searches. Our initial work on direct feature searches of digital medical imagery is outlined.

Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments.

PubMed

Linder, Suzanne K; Kamath, Geetanjali R; Pratt, Gregory F; Saraykar, Smita S; Volk, Robert J

2015-04-01

To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a health care decision-making instrument commonly used in clinical settings. We searched the literature using two methods: (1) keyword searching using variations of "Control Preferences Scale" and (2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, and Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Keyword searches in bibliographic databases yielded high average precision (90%) but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45-54%), but precision ranged from 35% to 75% with Scopus being the most precise. Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time, and resources should dictate the combination of which methods and databases are used. Copyright © 2015 Elsevier Inc. All rights reserved.

Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments

PubMed Central

Linder, Suzanne K.; Kamath, Geetanjali R.; Pratt, Gregory F.; Saraykar, Smita S.; Volk, Robert J.

2015-01-01

Objective To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a healthcare decision-making instrument commonly used in clinical settings. Study Design & Setting We searched the literature using two methods: 1) keyword searching using variations of “control preferences scale” and 2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Results Keyword searches in bibliographic databases yielded high average precision (90%), but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45–54%), but precision ranged from 35–75% with Scopus being the most precise. Conclusion Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time and resources should dictate the combination of which methods and databases are used. PMID:25554521

VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

NASA Technical Reports Server (NTRS)

Roussopoulos, N.; Sellis, Timos

1992-01-01

One of biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental database access method, VIEWCACHE, provides such an interface for accessing distributed data sets and directories. VIEWCACHE allows database browsing and search performing inter-database cross-referencing with no actual data movement between database sites. This organization and processing is especially suitable for managing Astrophysics databases which are physically distributed all over the world. Once the search is complete, the set of collected pointers pointing to the desired data are cached. VIEWCACHE includes spatial access methods for accessing image data sets, which provide much easier query formulation by referring directly to the image and very efficient search for objects contained within a two-dimensional window. We will develop and optimize a VIEWCACHE External Gateway Access to database management systems to facilitate distributed database search.

Evaluation of Federated Searching Options for the School Library

ERIC Educational Resources Information Center

Abercrombie, Sarah E.

2008-01-01

Three hosted federated search tools, Follett One Search, Gale PowerSearch Plus, and WebFeat Express, were configured and implemented in a school library. Databases from five vendors and the OPAC were systematically searched. Federated search results were compared with each other and to the results of the same searches in the database's native…

Very Slow Search and Reach: Failure to Maximize Expected Gain in an Eye-Hand Coordination Task

PubMed Central

Zhang, Hang; Morvan, Camille; Etezad-Heydari, Louis-Alexandre; Maloney, Laurence T.

2012-01-01

We examined an eye-hand coordination task where optimal visual search and hand movement strategies were inter-related. Observers were asked to find and touch a target among five distractors on a touch screen. Their reward for touching the target was reduced by an amount proportional to how long they took to locate and reach to it. Coordinating the eye and the hand appropriately would markedly reduce the search-reach time. Using statistical decision theory we derived the sequence of interrelated eye and hand movements that would maximize expected gain and we predicted how hand movements should change as the eye gathered further information about target location. We recorded human observers' eye movements and hand movements and compared them with the optimal strategy that would have maximized expected gain. We found that most observers failed to adopt the optimal search-reach strategy. We analyze and describe the strategies they did adopt. PMID:23071430

Expert searching in public health

PubMed Central

Alpi, Kristine M.

2005-01-01

Objective: The article explores the characteristics of public health information needs and the resources available to address those needs that distinguish it as an area of searching requiring particular expertise. Methods: Public health searching activities from reference questions and literature search requests at a large, urban health department library were reviewed to identify the challenges in finding relevant public health information. Results: The terminology of the information request frequently differed from the vocabularies available in the databases. Searches required the use of multiple databases and/or Web resources with diverse interfaces. Issues of the scope and features of the databases relevant to the search questions were considered. Conclusion: Expert searching in public health differs from other types of expert searching in the subject breadth and technical demands of the databases to be searched, the fluidity and lack of standardization of the vocabulary, and the relative scarcity of high-quality investigations at the appropriate level of geographic specificity. Health sciences librarians require a broad exposure to databases, gray literature, and public health terminology to perform as expert searchers in public health. PMID:15685281

Online Patent Searching: The Realities.

ERIC Educational Resources Information Center

Kaback, Stuart M.

1983-01-01

Considers patent subject searching capabilities of major online databases, noting patent claims, "deep-indexed" files, test searches, retrieval of related references, multi-database searching, improvements needed in indexing of chemical structures, full text searching, improvements needed in handling numerical data, and augmenting a…

Reflections on mirror therapy: a systematic review of the effect of mirror visual feedback on the brain.

PubMed

Deconinck, Frederik J A; Smorenburg, Ana R P; Benham, Alex; Ledebt, Annick; Feltham, Max G; Savelsbergh, Geert J P

2015-05-01

Mirror visual feedback (MVF), a phenomenon where movement of one limb is perceived as movement of the other limb, has the capacity to alleviate phantom limb pain or promote motor recovery of the upper limbs after stroke. The tool has received great interest from health professionals; however, a clear understanding of the mechanisms underlying the neural recovery owing to MVF is lacking. We performed a systematic review to assess the effect of MVF on brain activation during a motor task. We searched PubMed, CINAHL, and EMBASE databases for neuroimaging studies investigating the effect of MVF on the brain. Key details for each study regarding participants, imaging methods, and results were extracted. The database search yielded 347 article, of which we identified 33 suitable for inclusion. Compared with a control condition, MVF increases neural activity in areas involved with allocation of attention and cognitive control (dorsolateral prefrontal cortex, posterior cingulate cortex, S1 and S2, precuneus). Apart from activation in the superior temporal gyrus and premotor cortex, there is little evidence that MVF activates the mirror neuron system. MVF increases the excitability of the ipsilateral primary motor cortex (M1) that projects to the "untrained" hand/arm. There is also evidence for ipsilateral projections from the contralateral M1 to the untrained/affected hand as a consequence of training with MVF. MVF can exert a strong influence on the motor network, mainly through increased cognitive penetration in action control, though the variance in methodology and the lack of studies that shed light on the functional connectivity between areas still limit insight into the actual underlying mechanisms. © The Author(s) 2014.

Using "Reader's Guide to Periodical Literature" on CD-Rom To Teach Database Searching to High School Students.

ERIC Educational Resources Information Center

Kern, Joanne F.

The lack of opportunity for high school sophomores to learn database searching was addressed by the implementation of a computerized magazine article search program. "Reader's Guide to Periodical Literature" on CD-ROM was used to train students in database searching during the time they were assigned to the library to do research papers…

Psychological therapies for sickle cell disease and pain.

PubMed

Anie, K A; Green, J

2002-01-01

Sickle cell disease comprises a group of genetic blood disorders, and occurs when the sickle haemoglobin gene is inherited from both parents. The effects of the condition are: varying degrees of anaemia which if severe reduce the capacity for mobility; predisposition to obstruction of small blood capillaries causing pain in muscle and bone known as "crises"; damage to major organs such as the spleen, liver, kidneys, and lungs; and increased vulnerability to severe infections. There are both medical and non-medical complications, and treatment is usually symptomatic and palliative in nature. Psychological intervention for individuals with sickle cell disease seems viable in complementing current medical treatment, and studies examining their efficacy appear to have also yielded encouraging results. To examine the evidence that in patients with sickle cell disease, psychological treatment improves the ability to cope with the condition. The Cochrane Cystic Fibrosis and Genetic Disorders Group specialist trials register which comprises references from comprehensive electronic database searches. Also, hand searching relevant journals, hand searching abstract books of conference proceedings, and searches on the Internet were performed. Date of the most recent search of the Group's specialised register: January 2001. All randomised or quasi-randomised controlled trials comparing the use of psychological intervention to no (psychological) intervention in patients with sickle cell disease. Both reviewers independently extracted data and assessed trial quality. Five studies were identified in the initial search, of which three studies, with a total of 158 patients were eligible for inclusion in the review. Published data reveal that family education and cognitive behavioural therapy can help patients cope with sickle cell disease. Patient education programmes improve knowledge and attitudes of patients with sickle cell disease. There is as yet however, insufficient evidence to demonstrate the role of other psychological therapies. This systematic review has clearly identified the need for well-designed, adequately powered, multicentre randomised controlled trials assessing the effectiveness of specific intervention in sickle cell disease.

Application of kernel functions for accurate similarity search in large chemical databases.

PubMed

Wang, Xiaohong; Huan, Jun; Smalter, Aaron; Lushington, Gerald H

2010-04-29

Similarity search in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed that structure based methods provide an efficient way to do the query. Recently various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models, graph kernel functions can not be applied to large chemical compound database due to the high computational complexity and the difficulties in indexing similarity search for large databases. To bridge graph kernel function and similarity search in chemical databases, we applied a novel kernel-based similarity measurement, developed in our team, to measure similarity of graph represented chemicals. In our method, we utilize a hash table to support new graph kernel function definition, efficient storage and fast search. We have applied our method, named G-hash, to large chemical databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Moreover, the similarity measurement and the index structure is scalable to large chemical databases with smaller indexing size, and faster query processing time as compared to state-of-the-art indexing methods such as Daylight fingerprints, C-tree and GraphGrep. Efficient similarity query processing method for large chemical databases is challenging since we need to balance running time efficiency and similarity search accuracy. Our previous similarity search method, G-hash, provides a new way to perform similarity search in chemical databases. Experimental study validates the utility of G-hash in chemical databases.

Algorithms for database-dependent search of MS/MS data.

PubMed

Matthiesen, Rune

2013-01-01

The frequent used bottom-up strategy for identification of proteins and their associated modifications generate nowadays typically thousands of MS/MS spectra that normally are matched automatically against a protein sequence database. Search engines that take as input MS/MS spectra and a protein sequence database are referred as database-dependent search engines. Many programs both commercial and freely available exist for database-dependent search of MS/MS spectra and most of the programs have excellent user documentation. The aim here is therefore to outline the algorithm strategy behind different search engines rather than providing software user manuals. The process of database-dependent search can be divided into search strategy, peptide scoring, protein scoring, and finally protein inference. Most efforts in the literature have been put in to comparing results from different software rather than discussing the underlining algorithms. Such practical comparisons can be cluttered by suboptimal implementation and the observed differences are frequently caused by software parameters settings which have not been set proper to allow even comparison. In other words an algorithmic idea can still be worth considering even if the software implementation has been demonstrated to be suboptimal. The aim in this chapter is therefore to split the algorithms for database-dependent searching of MS/MS data into the above steps so that the different algorithmic ideas become more transparent and comparable. Most search engines provide good implementations of the first three data analysis steps mentioned above, whereas the final step of protein inference are much less developed for most search engines and is in many cases performed by an external software. The final part of this chapter illustrates how protein inference is built into the VEMS search engine and discusses a stand-alone program SIR for protein inference that can import a Mascot search result.

Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

PubMed

Mackey, Aaron J; Pearson, William R

2004-10-01

Relational databases are designed to integrate diverse types of information and manage large sets of search results, greatly simplifying genome-scale analyses. Relational databases are essential for management and analysis of large-scale sequence analyses, and can also be used to improve the statistical significance of similarity searches by focusing on subsets of sequence libraries most likely to contain homologs. This unit describes using relational databases to improve the efficiency of sequence similarity searching and to demonstrate various large-scale genomic analyses of homology-related data. This unit describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. These include basic use of the database to generate a novel sequence library subset, how to extend and use seqdb_demo for the storage of sequence similarity search results and making use of various kinds of stored search results to address aspects of comparative genomic analysis.

DNA profiles, computer searches, and the Fourth Amendment.

PubMed

Kimel, Catherine W

2013-01-01

Pursuant to federal statutes and to laws in all fifty states, the United States government has assembled a database containing the DNA profiles of over eleven million citizens. Without judicial authorization, the government searches each of these profiles one-hundred thousand times every day, seeking to link database subjects to crimes they are not suspected of committing. Yet, courts and scholars that have addressed DNA databasing have focused their attention almost exclusively on the constitutionality of the government's seizure of the biological samples from which the profiles are generated. This Note fills a gap in the scholarship by examining the Fourth Amendment problems that arise when the government searches its vast DNA database. This Note argues that each attempt to match two DNA profiles constitutes a Fourth Amendment search because each attempted match infringes upon database subjects' expectations of privacy in their biological relationships and physical movements. The Note further argues that database searches are unreasonable as they are currently conducted, and it suggests an adaptation of computer-search procedures to remedy the constitutional deficiency.

Chapter 51: How to Build a Simple Cone Search Service Using a Local Database

NASA Astrophysics Data System (ADS)

Kent, B. R.; Greene, G. R.

The cone search service protocol will be examined from the server side in this chapter. A simple cone search service will be setup and configured locally using MySQL. Data will be read into a table, and the Java JDBC will be used to connect to the database. Readers will understand the VO cone search specification and how to use it to query a database on their local systems and return an XML/VOTable file based on an input of RA/DEC coordinates and a search radius. The cone search in this example will be deployed as a Java servlet. The resulting cone search can be tested with a verification service. This basic setup can be used with other languages and relational databases.

muBLASTP: database-indexed protein sequence search on multicore CPUs.

PubMed

Zhang, Jing; Misra, Sanchit; Wang, Hao; Feng, Wu-Chun

2016-11-04

The Basic Local Alignment Search Tool (BLAST) is a fundamental program in the life sciences that searches databases for sequences that are most similar to a query sequence. Currently, the BLAST algorithm utilizes a query-indexed approach. Although many approaches suggest that sequence search with a database index can achieve much higher throughput (e.g., BLAT, SSAHA, and CAFE), they cannot deliver the same level of sensitivity as the query-indexed BLAST, i.e., NCBI BLAST, or they can only support nucleotide sequence search, e.g., MegaBLAST. Due to different challenges and characteristics between query indexing and database indexing, the existing techniques for query-indexed search cannot be used into database indexed search. muBLASTP, a novel database-indexed BLAST for protein sequence search, delivers identical hits returned to NCBI BLAST. On Intel Haswell multicore CPUs, for a single query, the single-threaded muBLASTP achieves up to a 4.41-fold speedup for alignment stages, and up to a 1.75-fold end-to-end speedup over single-threaded NCBI BLAST. For a batch of queries, the multithreaded muBLASTP achieves up to a 5.7-fold speedups for alignment stages, and up to a 4.56-fold end-to-end speedup over multithreaded NCBI BLAST. With a newly designed index structure for protein database and associated optimizations in BLASTP algorithm, we re-factored BLASTP algorithm for modern multicore processors that achieves much higher throughput with acceptable memory footprint for the database index.

Associations of work activities requiring pinch or hand grip or exposure to hand-arm vibration with finger and wrist osteoarthritis: a meta-analysis.

PubMed

Hammer, Paula E C; Shiri, Rahman; Kryger, Ann I; Kirkeskov, Lilli; Bonde, Jens Peter

2014-03-01

We systematically reviewed the epidemiologic evidence linking finger and wrist osteoarthritis (OA) with work activities requiring pinch or hand grip or exposure to hand-arm vibration (HAV). PubMed and Embase databases were searched up to June 2013. We selected studies assessing the associations of radiographic diagnosed finger and/or wrist joint OA with work activities involving pinch or hand grip or exposure to HAV. We used specific criteria to evaluate completeness of reporting, potential confounding, and bias. Pooled odds ratios (OR) were computed using random-effects meta-analyses. Of the 19 studies included, 17 were cross-sectional, 1 was a prospective cohort, and 1 a case-control study. The meta-analyses of studies that controlled their estimates for at least age and gender showed the associations of pinch grip work with proximal interphalangeal joint [OR 1.56, 95% confidence interval (95% CI) 1.09-2.23] and the first carpometacarpal joint OA (OR 2.10, 95% CI 1.06-4.17), but not with distal interphalangeal, metacarpalphalangeal, or wrist joints OA. Hand grip work and exposure to HAV were not associated with any finger or wrist OA. Epidemiological studies provide limited evidence that pinch grip may increase the risk of wrist or finger OA, but causal relation cannot be resolved because of cross-sectional designs and inadequate characterization of biomechanical strain to the hand and wrist.

Alternative Databases for Anthropology Searching.

ERIC Educational Resources Information Center

Brody, Fern; Lambert, Maureen

1984-01-01

Examines online search results of sample questions in several databases covering linguistics, cultural anthropology, and physical anthropology in order to determine if and where any overlap in results might occur, and which files have greatest number of relevant hits. Search results by database are given for each subject area. (EJS)

When is a search not a search? A comparison of searching the AMED complementary health database via EBSCOhost, OVID and DIALOG.

PubMed

Younger, Paula; Boddy, Kate

2009-06-01

The researchers involved in this study work at Exeter Health library and at the Complementary Medicine Unit, Peninsula School of Medicine and Dentistry (PCMD). Within this collaborative environment it is possible to access the electronic resources of three institutions. This includes access to AMED and other databases using different interfaces. The aim of this study was to investigate whether searching different interfaces to the AMED allied health and complementary medicine database produced the same results when using identical search terms. The following Internet-based AMED interfaces were searched: DIALOG DataStar; EBSCOhost and OVID SP_UI01.00.02. Search results from all three databases were saved in an endnote database to facilitate analysis. A checklist was also compiled comparing interface features. In our initial search, DIALOG returned 29 hits, OVID 14 and Ebsco 8. If we assume that DIALOG returned 100% of potential hits, OVID initially returned only 48% of hits and EBSCOhost only 28%. In our search, a researcher using the Ebsco interface to carry out a simple search on AMED would miss over 70% of possible search hits. Subsequent EBSCOhost searches on different subjects failed to find between 21 and 86% of the hits retrieved using the same keywords via DIALOG DataStar. In two cases, the simple EBSCOhost search failed to find any of the results found via DIALOG DataStar. Depending on the interface, the number of hits retrieved from the same database with the same simple search can vary dramatically. Some simple searches fail to retrieve a substantial percentage of citations. This may result in an uninformed literature review, research funding application or treatment intervention. In addition to ensuring that keywords, spelling and medical subject headings (MeSH) accurately reflect the nature of the search, database users should include wildcards and truncation and adapt their search strategy substantially to retrieve the maximum number of appropriate citations possible. Librarians should be aware of these differences when making purchasing decisions, carrying out literature searches and planning user education.

VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

NASA Technical Reports Server (NTRS)

Roussopoulos, N.; Sellis, Timos

1993-01-01

One of the biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental data base access method, VIEWCACHE, provides such an interface for accessing distributed datasets and directories. VIEWCACHE allows database browsing and search performing inter-database cross-referencing with no actual data movement between database sites. This organization and processing is especially suitable for managing Astrophysics databases which are physically distributed all over the world. Once the search is complete, the set of collected pointers pointing to the desired data are cached. VIEWCACHE includes spatial access methods for accessing image datasets, which provide much easier query formulation by referring directly to the image and very efficient search for objects contained within a two-dimensional window. We will develop and optimize a VIEWCACHE External Gateway Access to database management systems to facilitate database search.

Towards a model of surgeons' leadership in the operating room.

PubMed

Henrickson Parker, Sarah; Yule, Steven; Flin, Rhona; McKinley, Aileen

2011-07-01

There is widespread recognition that leadership skills are essential for effective performance in the workplace, but the evidence detailing effective leadership behaviours for surgeons during operations is unclear. Boolean searches of four on-line databases and detailed hand search of relevant references were conducted. A four stage screening process was adopted stipulating that articles presented empirical data on surgeons' intraoperative leadership behaviours. Ten relevant articles were identified and organised by method of investigation into (i) observation, (ii) questionnaire and (iii) interview studies. This review summarises the limited literature on surgeons' intraoperative leadership, and proposes a preliminary theoretically based structure for intraoperative leadership behaviours. This structure comprises seven categories with corresponding leadership components and covers two overarching themes related to task- and team-focus. Selected leadership theories which may be applicable to the operating room environment are also discussed. Further research is required to determine effective intraoperative leadership behaviours for safe surgical practice.

Online counseling: a narrative and critical review of the literature.

PubMed

Richards, Derek; Viganó, Noemi

2013-09-01

This article aimed to critically review the literature on online counseling. Database and hand-searches were made using search terms and eligibility criteria, yielding a total of 123 studies. The review begins with what characterizes online counseling. Outcome and process research in online counseling is reviewed. Features and cyberbehaviors of online counseling such as anonymity and disinhibition, convenience, time-delay, the loss of social signaling, and writing behavior in cyberspace are discussed. Ethical behavior, professional training, client suitability, and clients' and therapists' attitudes and experiences of online counseling are reviewed. A growing body of knowledge to date is positive in showing that online counseling can have a similar impact and is capable of replicating the facilitative conditions as face-to-face encounters. A need remains for stronger empirical evidence to establish efficacy and effectiveness and to understand better the unique mediating and facilitative variables. © 2013 Wiley Periodicals, Inc.

Prototype of Multifunctional Full-text Library in the Architecture Web-browser / Web-server / SQL-server

NASA Astrophysics Data System (ADS)

Lyapin, Sergey; Kukovyakin, Alexey

Within the framework of the research program "Textaurus" an operational prototype of multifunctional library T-Libra v.4.1. has been created which makes it possible to carry out flexible parametrizable search within a full-text database. The information system is realized in the architecture Web-browser / Web-server / SQL-server. This allows to achieve an optimal combination of universality and efficiency of text processing, on the one hand, and convenience and minimization of expenses for an end user (due to applying of a standard Web-browser as a client application), on the other one. The following principles underlie the information system: a) multifunctionality, b) intelligence, c) multilingual primary texts and full-text searching, d) development of digital library (DL) by a user ("administrative client"), e) multi-platform working. A "library of concepts", i.e. a block of functional models of semantic (concept-oriented) searching, as well as a subsystem of parametrizable queries to a full-text database, which is closely connected with the "library", serve as a conceptual basis of multifunctionality and "intelligence" of the DL T-Libra v.4.1. An author's paragraph is a unit of full-text searching in the suggested technology. At that, the "logic" of an educational / scientific topic or a problem can be built in a multilevel flexible structure of a query and the "library of concepts", replenishable by the developers and experts. About 10 queries of various level of complexity and conceptuality are realized in the suggested version of the information system: from simple terminological searching (taking into account lexical and grammatical paradigms of Russian) to several kinds of explication of terminological fields and adjustable two-parameter thematic searching (a [set of terms] and a [distance between terms] within the limits of an author's paragraph are such parameters correspondingly).

Database Searching by Managers.

ERIC Educational Resources Information Center

Arnold, Stephen E.

Managers and executives need the easy and quick access to business and management information that online databases can provide, but many have difficulty articulating their search needs to an intermediary. One possible solution would be to encourage managers and their immediate support staff members to search textual databases directly as they now…

Constructing Effective Search Strategies for Electronic Searching.

ERIC Educational Resources Information Center

Flanagan, Lynn; Parente, Sharon Campbell

Electronic databases have grown tremendously in both number and popularity since their development during the 1960s. Access to electronic databases in academic libraries was originally offered primarily through mediated search services by trained librarians; however, the advent of CD-ROM and end-user interfaces for online databases has shifted the…

Subject searching of monographs online in the medical literature.

PubMed

Brahmi, F A

1988-01-01

Searching by subject for monographic information online in the medical literature is a challenging task. The NLM database of choice is CATLINE. Other NLM databases of interest are BIOTHICSLINE, CANCERLIT, HEALTH, POPLINE, and TOXLINE. Ten BRS databases are also discussed. Of these, Books in Print, Bookinfo, and OCLC are explored further. The databases are compared as to number of total records and number and percentage of monographs. Three topics were searched on CROSS to compare hits on BBIP, BOOK, and OCLC. The same searches were run on CATLINE. The parameters of time coverage and language were equalized and the resulting citations were compared and analyzed for duplication and uniqueness. With the input of CATLINE tapes into OCLC, OCLC has become the database of choice for searching by subject for medical monographs.

mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

PubMed

Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

2018-05-21

With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

Strategies for expanding health insurance coverage in vulnerable populations

PubMed Central

Jia, Liying; Yuan, Beibei; Huang, Fei; Lu, Ying; Garner, Paul; Meng, Qingyue

2014-01-01

Background Health insurance has the potential to improve access to health care and protect people from the financial risks of diseases. However, health insurance coverage is often low, particularly for people most in need of protection, including children and other vulnerable populations. Objectives To assess the effectiveness of strategies for expanding health insurance coverage in vulnerable populations. Search methods We searched Cochrane Central Register of Controlled Trials (CENTRAL), part of The Cochrane Library. www.thecochranelibrary.com (searched 2 November 2012), PubMed (searched 1 November 2012), EMBASE (searched 6 July 2012), Global Health (searched 6 July 2012), IBSS (searched 6 July 2012), WHO Library Database (WHOLIS) (searched 1 November 2012), IDEAS (searched 1 November 2012), ISI-Proceedings (searched 1 November 2012),OpenGrey (changed from OpenSIGLE) (searched 1 November 2012), African Index Medicus (searched 1 November 2012), BLDS (searched 1 November 2012), Econlit (searched 1 November 2012), ELDIS (searched 1 November 2012), ERIC (searched 1 November 2012), HERDIN NeON Database (searched 1 November 2012), IndMED (searched 1 November 2012), JSTOR (searched 1 November 2012), LILACS(searched 1 November 2012), NTIS (searched 1 November 2012), PAIS (searched 6 July 2012), Popline (searched 1 November 2012), ProQuest Dissertation &Theses Database (searched 1 November 2012), PsycINFO (searched 6 July 2012), SSRN (searched 1 November 2012), Thai Index Medicus (searched 1 November 2012), World Bank (searched 2 November 2012), WanFang (searched 3 November 2012), China National Knowledge Infrastructure (CHKD-CNKI) (searched 2 November 2012). In addition, we searched the reference lists of included studies and carried out a citation search for the included studies via Web of Science to find other potentially relevant studies. Selection criteria Randomised controlled trials (RCTs), non-randomised controlled trials (NRCTs), controlled before-after (CBA) studies and Interrupted time series (ITS) studies that evaluated the effects of strategies on increasing health insurance coverage for vulnerable populations. We defined strategies as measures to improve the enrolment of vulnerable populations into health insurance schemes. Two categories and six specified strategies were identified as the interventions. Data collection and analysis At least two review authors independently extracted data and assessed the risk of bias. We undertook a structured synthesis. Main results We included two studies, both from the United States. People offered health insurance information and application support by community-based case managers were probably more likely to enrol their children into health insurance programmes (risk ratio (RR) 1.68, 95% confidence interval (CI) 1.44 to 1.96, moderate quality evidence) and were probably more likely to continue insuring their children (RR 2.59, 95% CI 1.95 to 3.44, moderate quality evidence). Of all the children that were insured, those in the intervention group may have been insured quicker (47.3 fewer days, 95% CI 20.6 to 74.0 fewer days, low quality evidence) and parents may have been more satisfied on average (satisfaction score average difference 1.07, 95% CI 0.72 to 1.42, low quality evidence). In the second study applications were handed out in emergency departments at hospitals, compared to not handing out applications, and may have had an effect on enrolment (RR 1.5, 95% CI 1.03 to 2.18, low quality evidence). Authors' conclusions Community-based case managers who provide health insurance information, application support, and negotiate with the insurer probably increase enrolment of children in health insurance schemes. However, the transferability of this intervention to other populations or other settings is uncertain. Handing out insurance application materials in hospital emergency departments may help increase the enrolment of children in health insurance schemes. Further studies evaluating the effectiveness of different strategies for expanding health insurance coverage in vulnerable population are needed in different settings, with careful attention given to study design. PLAIN LANGUAGE SUMMARY Strategies for expanding health insurance coverage in vulnerable populations Researchers in The Cochrane Collaboration conducted a review of the effect of strategies to increase the number of people from vulnerable populations that are enrolled into health insurance programmes. They searched for all relevant studies and found two studies. Their findings are summarised below. What is a health insurance programme? Governments in many countries offer healthcare services at low rates or free of charge to all their citizens, often paying for these services through taxes. However, in many developing countries and some developed countries this is not the case. In these countries, many people get their healthcare expenses covered through government health insurance programmes, which are often paid for through membership fees. But certain groups of people, such as children, the elderly, women, people with low incomes, people living in rural areas, racial and ethnic minorities, immigrants, and people with chronic diseases or disabilities, are less likely to be members of these programmes even though they are more likely to have health problems. In some of these countries governments have tried to make sure that health insurance programmes cover these vulnerable groups. One way of doing this is to improve the design of the programme. For instance, governments can change the rules for who can join the programme or they can make it cheaper to join. But even if a programme is well-designed, people may still not join it. For instance, they may not know that they can become members or they may find the application process too difficult. To address these problems, for instance, governments can give people more information about the programme and who can join, or can make the application process easier. What this research says Both studies in this review took place in the USA and were aimed at uninsured children. In the first study, case managers contacted the families of uninsured Latin American children, gave them information about health insurance, helped them apply, and helped them appeal when a wrong decision was made. In the second study, insurance application forms were handed out to the families of children visiting hospital emergency departments. In both studies, these families were compared to families who were not given additional information or support. The studies showed the following: People who are offered health insurance information and application support: - are probably more likely to enrol their children into health insurance programmes (moderate quality evidence); - are probably more likely to continue insuring their children (moderate quality evidence); - may be quicker at getting insurance (low quality evidence); - may be more satisfied with the process of enrolment (low quality evidence). People who are given insurance application forms in the emergency departments of hospitals: - may be more likely to enrol their children into health insurance programmes (low quality evidence). No unwanted effects were reported in the studies. A possible unwanted effect might be that people could experience the information and support as annoying or unhelpful. However, in the one study that measured the parents' satisfaction, people were more satisfied when given information and support. PMID:25425010

Search Fermilab Plant Database

Science.gov Websites

Select the characteristics of the plant you want to find below and click the Search button. To see Plants to see all the prairie plants in the database. Click Search All Plants at Fermilab to search for reflects observations at Fermilab. If you need a more sophisticated search, try the Advanced Search. Search

Reducing process delays for real-time earthquake parameter estimation - An application of KD tree to large databases for Earthquake Early Warning

NASA Astrophysics Data System (ADS)

Yin, Lucy; Andrews, Jennifer; Heaton, Thomas

2018-05-01

Earthquake parameter estimations using nearest neighbor searching among a large database of observations can lead to reliable prediction results. However, in the real-time application of Earthquake Early Warning (EEW) systems, the accurate prediction using a large database is penalized by a significant delay in the processing time. We propose to use a multidimensional binary search tree (KD tree) data structure to organize large seismic databases to reduce the processing time in nearest neighbor search for predictions. We evaluated the performance of KD tree on the Gutenberg Algorithm, a database-searching algorithm for EEW. We constructed an offline test to predict peak ground motions using a database with feature sets of waveform filter-bank characteristics, and compare the results with the observed seismic parameters. We concluded that large database provides more accurate predictions of the ground motion information, such as peak ground acceleration, velocity, and displacement (PGA, PGV, PGD), than source parameters, such as hypocenter distance. Application of the KD tree search to organize the database reduced the average searching process by 85% time cost of the exhaustive method, allowing the method to be feasible for real-time implementation. The algorithm is straightforward and the results will reduce the overall time of warning delivery for EEW.

Medicinal Plants for the Treatment of Asthma: A Traditional Persian Medicine Perspective.

PubMed

Javadi, Behjat; Sahebkar, Amirhossein; Emami, Seyed Ahmad

2017-01-01

To search major Traditional Persian Medicine (TPM) textbooks for medicinal plants used to treat asthma. The conformity of the TPM findings on the anti-asthmatic efficacy of plants with the findings of pharmacological studies was also explored. Major TPM textbooks were hand searched to find medicinal plants used for the treatment of asthma. Scientific names of TPM-suggested plants were determined using botanical databases and were used for a multidatabase electronic search in PubMed, Scopus, ScienceDirect and Google Scholar databases. Then, the antiasthmatic effectiveness of TPM-recommended plants was verified in view of the findings from modern pharmacological investigations. According to the main TPM texts, Adianthum capillus-veneris, Boswellia oleogumresin, Crocus sativus, Glycyrrhiza glabra, Hyssopus officinalis and Ruta graveolens were the most efficacious medicinal plants for the treatment of asthma. This finding was confirmed by pharmacological studies which showed counterbalancing effects of the above-mentioned plants on inflammation, oxidative stress, allergic response, tracheal smooth muscle cell constriction and airway remodeling. The strong ethnobotanical background of plants used in TPM could be a valuable tool to find new anti-asthmatic medications. In this review, TPM-suggested anti-asthmatic plants were found to possess several mechanisms relevant to the treatment of respiratory diseases according to the information retrieved from modern pharmacological studies. This high degree of conformity suggested further proof-of-concept trials to ascertain the role of these plants in the routine management of asthmatic patients. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Why Cannot We have an Etiological Classification for the Patients with Granular Myringitis?

PubMed

Bansal, Mohan

2017-09-01

Though granular myringitis (GM) is not a very rare disease it does not have any classification. Its exact etiology is not known. The granulations on tympanic membrane also occur in association with other lesions of external auditory canal (EAC) and middle ear. The aims of this study were to know the etiological factors of GM and classify the disease according to its etiological factors and associated disorders of EAC and middle ear. Data were retrieved from the search of four electronic databases: PubMed, EMBASE, Cochrane Library, and Google scholar. Relevant articles were also sought by a hand search review of reference books. The databases were searched using the key words otitis externa, external otitis, granular myringitis, granular otitis externa and myringitis. Data were extracted using a pre-defined data-extraction form. The following data were recorded (1) etiological and predisposing conditions; (2) pathological features; (3) associated disorders of external and middle ear. The study proposes the etiological classification of GM. It suggests two major groups: primary and secondary. The primary GM is basically idiopathic and these patients do no have evidences of any other types of otitis media and otitis externa. In the secondary GM the cause is obvious and the patients usually have associated otitis media and/or lesions of external ear canal. Author speculates that habit of self ear cleaning/scratching is a specific etiological factor in cases of primary GM but more studies are required to confirm this theory.

A proposed protocol for hand and table sanitizing in chiropractic clinics and education institutions

PubMed Central

Evans, Marion Willard; Ramcharan, Michael; Floyd, Rod; Globe, Gary; Ndetan, Harrison; Williams, Ronald; Ivie, Ronald

2009-01-01

Abstract Objective By nature, chiropractic is a hands-on profession using manipulation applied to the joints with direct skin-to-skin contacts. Chiropractic tables are designed with a face piece to accommodate the prone patient's head in a neutral position and hand rests to allow for relaxed shoulders and upper spine so treatment is facilitated. The purpose of this article is to present a proposed guideline for hand and treatment table surface sanitizing for the chiropractic profession that is evidence-based and can easily be adopted by teaching institutions and doctors in the field. Methods A review of the chiropractic literature demonstrated that pathogenic microbes are present on treatment tables in teaching clinics at multiple facilities, yet no standardized protocols exist in the United States regarding table sanitizing and hand hygiene in chiropractic clinics or education institutions. This article reviews the scientific literature on the subject by using several search engines, databases, and specific reviews of documents pertaining to the topic including existing general guidelines. Results The literature has several existing guidelines that the authors used to develop a proposed protocol for hand and table sanitizing specific to the chiropractic profession. Recommendations were developed and are presented on hand hygiene and table sanitizing procedures that could lower the risk of infection for both clinical personnel and patients in chiropractic facilities. Conclusion This article offers a protocol for hand and table sanitizing in chiropractic clinics and education institutions. The chiropractic profession should consider adoption of these or similar measures and disseminate them to teaching clinics, institutions, and private practitioners. PMID:19646384

Do public access defibrillation (PAD) programmes lead to an increase of patients surviving to discharge from hospital following out of hospital cardiac arrest?--a literature review.

PubMed

Clare, Carl

2006-11-01

To ascertain the evidence for effectiveness of Public Access Defibrillation Programmes using any level of first responder. Structured searches were made of Medline, Cinahl, Embase, and 'All EBM reviews' (CDSR, ACP Journal Club, DARE, CCTR). No limits were set on the searches in terms of date, publication type or language. Limited hand searches were carried out and colleagues approached for potential papers. All 491 results were 'hand searched' for suitability. Potential papers for inclusion were further reviewed by access to abstracts or full text if necessary. The final papers for review were assessed using a recognised checklist. Of a total of 491 results from all databases removal of repeats and papers that did not answer the question led to 22 papers being further reviewed. Of these 19 were excluded and a final three were assessed and reviewed. Of the three papers two were randomised controlled trials (one with cross over design) and one was a non-randomised controlled cross over trial. Two of the papers assessed the use of level one responders and one level two responders. Odds ratios for the trials using level one responders were 1.3 and 1.6. The relative risk (of survival) for the trial using level two responders was 2.0. However all three trials had wide confidence intervals. The use of level one responders probably carries a slight benefit for patients in OOHCA. The use of level two responders may lead to a greater benefit but only for a small section of the population suffering OOHCA. Emphasis must also be placed on the improvement of ambulance response times and bystander CPR rates.

Interactive searching of facial image databases

NASA Astrophysics Data System (ADS)

Nicholls, Robert A.; Shepherd, John W.; Shepherd, Jean

1995-09-01

A set of psychological facial descriptors has been devised to enable computerized searching of criminal photograph albums. The descriptors have been used to encode image databased of up to twelve thousand images. Using a system called FACES, the databases are searched by translating a witness' verbal description into corresponding facial descriptors. Trials of FACES have shown that this coding scheme is more productive and efficient than searching traditional photograph albums. An alternative method of searching the encoded database using a genetic algorithm is currenly being tested. The genetic search method does not require the witness to verbalize a description of the target but merely to indicate a degree of similarity between the target and a limited selection of images from the database. The major drawback of FACES is that is requires a manual encoding of images. Research is being undertaken to automate the process, however, it will require an algorithm which can predict human descriptive values. Alternatives to human derived coding schemes exist using statistical classifications of images. Since databases encoded using statistical classifiers do not have an obvious direct mapping to human derived descriptors, a search method which does not require the entry of human descriptors is required. A genetic search algorithm is being tested for such a purpose.

Barriers to kidney transplants in Indonesia: a literature review.

PubMed

Bennett, P N; Hany, A

2009-03-01

People living with chronic kidney disease will require renal dialysis or a kidney transplant to maintain life. Although Indonesia has a developing healthcare industry, Indonesia's kidney transplant rates are lower than comparable nations. To explore the healthcare literature to identify barriers to kidney transplants in particular in relation to Indonesia. Healthcare databases were searched (CINAHL, Medline, EBSCOhostEJS, Blackwell Synergy, Web of Science, PubMed, Google Scholar and Proquest 5000) using the search terms: transplant, kidney disease, renal, dialysis, haemodialysis, Indonesia and nursing. The search was limited to English and Indonesian language data sources from 1997 to 2007. Reference lists of salient academic articles were hand searched. The results of our search identified six articles that met our criteria. Costs are the major barrier to kidney transplant in Indonesia, followed by cultural beliefs, perception of the law, lack of information and lack of infrastructure. In addition, kidney disease prevention strategies are required. There are many complex socio-economic, geographical, legal, cultural and religious factors that contribute to low kidney transplant rates in Indonesia. Although an increase in transplantation rates will require strategies from various agencies, healthcare professionals, including nurses, can play a role in overcoming some barriers. Community education programmes, improving their own education levels and by increasing empowerment in nursing we may contribute to improved kidney transplant rates in Indonesia.

Searching Harvard Business Review Online. . . Lessons in Searching a Full Text Database.

ERIC Educational Resources Information Center

Tenopir, Carol

1985-01-01

This article examines the Harvard Business Review Online (HBRO) database (bibliographic description fields, abstracts, extracted information, full text, subject descriptors) and reports on 31 sample HBRO searches conducted in Bibliographic Retrieval Services to test differences between searching full text and searching bibliographic record. Sample…

FilTer BaSe: A web accessible chemical database for small compound libraries.

PubMed

Kolte, Baban S; Londhe, Sanjay R; Solanki, Bhushan R; Gacche, Rajesh N; Meshram, Rohan J

2018-03-01

Finding novel chemical agents for targeting disease associated drug targets often requires screening of large number of new chemical libraries. In silico methods are generally implemented at initial stages for virtual screening. Filtering of such compound libraries on physicochemical and substructure ground is done to ensure elimination of compounds with undesired chemical properties. Filtering procedure, is redundant, time consuming and requires efficient bioinformatics/computer manpower along with high end software involving huge capital investment that forms a major obstacle in drug discovery projects in academic setup. We present an open source resource, FilTer BaSe- a chemoinformatics platform (http://bioinfo.net.in/filterbase/) that host fully filtered, ready to use compound libraries with workable size. The resource also hosts a database that enables efficient searching the chemical space of around 348,000 compounds on the basis of physicochemical and substructure properties. Ready to use compound libraries and database presented here is expected to aid a helping hand for new drug developers and medicinal chemists. Copyright © 2017 Elsevier Inc. All rights reserved.

In search of the emotional face: anger versus happiness superiority in visual search.

PubMed

Savage, Ruth A; Lipp, Ottmar V; Craig, Belinda M; Becker, Stefanie I; Horstmann, Gernot

2013-08-01

Previous research has provided inconsistent results regarding visual search for emotional faces, yielding evidence for either anger superiority (i.e., more efficient search for angry faces) or happiness superiority effects (i.e., more efficient search for happy faces), suggesting that these results do not reflect on emotional expression, but on emotion (un-)related low-level perceptual features. The present study investigated possible factors mediating anger/happiness superiority effects; specifically search strategy (fixed vs. variable target search; Experiment 1), stimulus choice (Nimstim database vs. Ekman & Friesen database; Experiments 1 and 2), and emotional intensity (Experiment 3 and 3a). Angry faces were found faster than happy faces regardless of search strategy using faces from the Nimstim database (Experiment 1). By contrast, a happiness superiority effect was evident in Experiment 2 when using faces from the Ekman and Friesen database. Experiment 3 employed angry, happy, and exuberant expressions (Nimstim database) and yielded anger and happiness superiority effects, respectively, highlighting the importance of the choice of stimulus materials. Ratings of the stimulus materials collected in Experiment 3a indicate that differences in perceived emotional intensity, pleasantness, or arousal do not account for differences in search efficiency. Across three studies, the current investigation indicates that prior reports of anger or happiness superiority effects in visual search are likely to reflect on low-level visual features associated with the stimulus materials used, rather than on emotion. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Genetic Testing Registry

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

Database Search Strategies & Tips. Reprints from the Best of "ONLINE" [and]"DATABASE."

ERIC Educational Resources Information Center

Online, Inc., Weston, CT.

Reprints of 17 articles presenting strategies and tips for searching databases online appear in this collection, which is one in a series of volumes of reprints from "ONLINE" and "DATABASE" magazines. Edited for information professionals who use electronically distributed databases, these articles address such topics as: (1)…

Human Flesh Search Engine and Online Privacy.

PubMed

Zhang, Yang; Gao, Hong

2016-04-01

Human flesh search engine can be a double-edged sword, bringing convenience on the one hand and leading to infringement of personal privacy on the other hand. This paper discusses the ethical problems brought about by the human flesh search engine, as well as possible solutions.

An exploration of self-management support in the context of palliative nursing: a modified concept analysis

PubMed Central

2014-01-01

Background The role of self-management is often ambiguous, yet, it is an important area in clinical practice for palliative nurses. A clear conceptual understanding, however, of what it represents is lacking. Method This paper reports an analysis of the concept of self-management support in palliative nursing. Avant and Walker’s method was used to guide this concept analysis. A search of electronic databases (1990–2013), use of internet search engines and supplementary hand searching produced an international data set of reviews, empirical research, editorials, protocols and guidelines. Results Based on the analysis self-management support in palliative nursing has been defined as assessing, planning, and implementing appropriate care to enable the patient to live until they die and supporting the patient to be given the means to master or deal with their illness or their effects of their illness themselves. Conclusions Clarity with the concept of self-management support and palliative nursing could enable nurses to provide more patient and family centred care to people facing life threatening illnesses. PMID:25120381

Observer roles that optimise learning in healthcare simulation education: a systematic review.

PubMed

O'Regan, Stephanie; Molloy, Elizabeth; Watterson, Leonie; Nestel, Debra

2016-01-01

Simulation is widely used in health professional education. The convention that learners are actively involved may limit access to this educational method. The aim of this paper is to review the evidence for learning methods that employ directed observation as an alternative to hands-on participation in scenario-based simulation training. We sought studies that included either direct comparison of the learning outcomes of observers with those of active participants or identified factors important for the engagement of observers in simulation. We systematically searched health and education databases and reviewed journals and bibliographies for studies investigating or referring to observer roles in simulation using mannequins, simulated patients or role play simulations. A quality framework was used to rate the studies. We sought studies that included either direct comparison of the learning outcomes of observers with those of active participants or identified factors important for the engagement of observers in simulation. We systematically searched health and education databases and reviewed journals and bibliographies for studies investigating or referring to observer roles in simulation using mannequins, simulated patients or role play simulations. A quality framework was used to rate the studies. Nine studies met the inclusion criteria. Five studies suggest learning outcomes in observer roles are as good or better than hands-on roles in simulation. Four studies document learner satisfaction in observer roles. Five studies used a tool to guide observers. Eight studies involved observers in the debrief. Learning and satisfaction in observer roles is closely associated with observer tools, learner engagement, role clarity and contribution to the debrief. Learners that valued observer roles described them as affording an overarching view, examination of details from a distance, and meaningful feedback during the debrief. Learners who did not value observer roles described them as passive, or boring when compared to hands-on engagement in the simulation encounter. Learning outcomes and role satisfaction for observers is improved through learner engagement and the use of observer tools. The value that students attach to observer roles appear contingent on role clarity, use of observer tools, and inclusion of observers' perspectives in the debrief.

Can nutrition be promoted through agriculture-led food price policies? A systematic review

PubMed Central

Dangour, Alan D; Hawkesworth, Sophie; Shankar, Bhavani; Watson, Louise; Srinivasan, C S; Morgan, Emily H; Haddad, Lawrence; Waage, Jeff

2013-01-01

Objective To systematically review the available evidence on whether national or international agricultural policies that directly affect the price of food influence the prevalence rates of undernutrition or nutrition-related chronic disease in children and adults. Design Systematic review. Setting Global. Search strategy We systematically searched five databases for published literature (MEDLINE, EconLit, Agricola, AgEcon Search, Scopus) and systematically browsed other databases and relevant organisational websites for unpublished literature. Reference lists of included publications were hand-searched for additional relevant studies. We included studies that evaluated or simulated the effects of national or international food-price-related agricultural policies on nutrition outcomes reporting data collected after 1990 and published in English. Primary and secondary outcomes Prevalence rates of undernutrition (measured with anthropometry or clinical deficiencies) and overnutrition (obesity and nutrition-related chronic diseases including cancer, heart disease and diabetes). Results We identified a total of four relevant reports; two ex post evaluations and two ex ante simulations. A study from India reported on the undernutrition rates in children, and the other three studies from Egypt, the Netherlands and the USA reported on the nutrition-related chronic disease outcomes in adults. Two of the studies assessed the impact of policies that subsidised the price of agricultural outputs and two focused on public food distribution policies. The limited evidence base provided some support for the notion that agricultural policies that change the prices of foods at a national level can have an effect on population-level nutrition and health outcomes. Conclusions A systematic review of the available literature suggests that there is a paucity of robust direct evidence on the impact of agricultural price policies on nutrition and health. PMID:23801712

Assigning statistical significance to proteotypic peptides via database searches

PubMed Central

Alves, Gelio; Ogurtsov, Aleksey Y.; Yu, Yi-Kuo

2011-01-01

Querying MS/MS spectra against a database containing only proteotypic peptides reduces data analysis time due to reduction of database size. Despite the speed advantage, this search strategy is challenged by issues of statistical significance and coverage. The former requires separating systematically significant identifications from less confident identifications, while the latter arises when the underlying peptide is not present, due to single amino acid polymorphisms (SAPs) or post-translational modifications (PTMs), in the proteotypic peptide libraries searched. To address both issues simultaneously, we have extended RAId’s knowledge database to include proteotypic information, utilized RAId’s statistical strategy to assign statistical significance to proteotypic peptides, and modified RAId’s programs to allow for consideration of proteotypic information during database searches. The extended database alleviates the coverage problem since all annotated modifications, even those occurred within proteotypic peptides, may be considered. Taking into account the likelihoods of observation, the statistical strategy of RAId provides accurate E-value assignments regardless whether a candidate peptide is proteotypic or not. The advantage of including proteotypic information is evidenced by its superior retrieval performance when compared to regular database searches. PMID:21055489

National Center for Biotechnology Information

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

Information sources for obesity prevention policy research: a review of systematic reviews.

PubMed

Hanneke, Rosie; Young, Sabrina K

2017-08-08

Systematic identification of evidence in health policy can be time-consuming and challenging. This study examines three questions pertaining to systematic reviews on obesity prevention policy, in order to identify the most efficient search methods: (1) What percentage of the primary studies selected for inclusion in the reviews originated in scholarly as opposed to gray literature? (2) How much of the primary scholarly literature in this topic area is indexed in PubMed/MEDLINE? (3) Which databases index the greatest number of primary studies not indexed in PubMed, and are these databases searched consistently across systematic reviews? We identified systematic reviews on obesity prevention policy and explored their search methods and citations. We determined the percentage of scholarly vs. gray literature cited, the most frequently cited journals, and whether each primary study was indexed in PubMed. We searched 21 databases for all primary study articles not indexed in PubMed to determine which database(s) indexed the highest number of these relevant articles. In total, 21 systematic reviews were identified. Ten of the 21 systematic reviews reported searching gray literature, and 12 reviews ultimately included gray literature in their analyses. Scholarly articles accounted for 577 of the 649 total primary study papers. Of these, 495 (76%) were indexed in PubMed. Google Scholar retrieved the highest number of the remaining 82 non-PubMed scholarly articles, followed by Scopus and EconLit. The Journal of the American Dietetic Association was the most-cited journal. Researchers can maximize search efficiency by searching a small yet targeted selection of both scholarly and gray literature resources. A highly sensitive search of PubMed and those databases that index the greatest number of relevant articles not indexed in PubMed, namely multidisciplinary and economics databases, could save considerable time and effort. When combined with a gray literature search and additional search methods, including cited reference searching and consulting with experts, this approach could help maintain broad retrieval of relevant studies while improving search efficiency. Findings also have implications for designing specialized databases for public health research.

Transterm—extended search facilities and improved integration with other databases

PubMed Central

Jacobs, Grant H.; Stockwell, Peter A.; Tate, Warren P.; Brown, Chris M.

2006-01-01

Transterm has now been publicly available for >10 years. Major changes have been made since its last description in this database issue in 2002. The current database provides data for key regions of mRNA sequences, a curated database of mRNA motifs and tools to allow users to investigate their own motifs or mRNA sequences. The key mRNA regions database is derived computationally from Genbank. It contains 3′ and 5′ flanking regions, the initiation and termination signal context and coding sequence for annotated CDS features from Genbank and RefSeq. The database is non-redundant, enabling summary files and statistics to be prepared for each species. Advances include providing extended search facilities, the database may now be searched by BLAST in addition to regular expressions (patterns) allowing users to search for motifs such as known miRNA sequences, and the inclusion of RefSeq data. The database contains >40 motifs or structural patterns important for translational control. In this release, patterns from UTRsite and Rfam are also incorporated with cross-referencing. Users may search their sequence data with Transterm or user-defined patterns. The system is accessible at . PMID:16381889

Beliefs, Knowledge, Implementation, and Integration of Evidence-Based Practice Among Primary Health Care Providers: Protocol for a Scoping Review.

PubMed

Pereira, Filipa; Salvi, Mireille; Verloo, Henk

2017-08-01

The adoption of evidence-based practice (EBP) is promoted because it is widely recognized for improving the quality and safety of health care for patients, and reducing avoidable costs. Providers of primary care face numerous challenges to ensuring the effectiveness of their daily practices. Primary health care is defined as: the entry level into a health care services system, providing a first point of contact for all new needs and problems; patient-focused (not disease-oriented) care over time; care for all but the most uncommon or unusual conditions; and coordination or integration of care, regardless of where or by whom that care is delivered. Primary health care is the principal means by which to approach the main goal of any health care services system: optimization of health status. This review aims to scope publications examining beliefs, knowledge, implementation, and integration of EBPs among primary health care providers (HCPs). We will conduct a systematic scoping review of published articles in the following electronic databases, from their start dates until March 31, 2017: Medical Literature Analysis and Retrieval System Online (MEDLINE) via PubMed (from 1946), Embase (from 1947), Cumulative Index to Nursing and Allied Health Literature (CINAHL; from 1937), the Cochrane Central Register of Controlled Trials (CENTRAL; from 1992), PsycINFO (from 1806), Web of Science (from 1900), Joanna Briggs Institute (JBI) database (from 1998), Database of Abstracts of Reviews of Effects (DARE; from 1996), Trip medical database (from 1997), and relevant professional scientific journals (from their start dates). We will use the predefined search terms of, "evidence-based practice" and, "primary health care" combined with other terms, such as, "beliefs", "knowledge", "implementation", and "integration". We will also conduct a hand search of the bibliographies of all relevant articles and a search for unpublished studies using Google Scholar, ProQuest, Mednar, and WorldCat. We will consider publications in English, French, Spanish, and Portuguese. The electronic database searches were completed in April 2017. Retrieved articles are currently being screened, and the entire study is expected to be completed by November 2017. This systematic scoping review will provide a greater understanding of the beliefs, knowledge, implementation, and integration of EBPs among primary HCPs. The findings will inform clinical practice and help to draw a global picture of the EBP research topics that are relevant to primary care providers. ©Filipa Pereira, Mireille Salvi, Henk Verloo. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 01.08.2017.

LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences.

PubMed

Kirmitzoglou, Ioannis; Promponas, Vasilis J

2015-07-01

Local compositionally biased and low complexity regions (LCRs) in amino acid sequences have initially attracted the interest of researchers due to their implication in generating artifacts in sequence database searches. There is accumulating evidence of the biological significance of LCRs both in physiological and in pathological situations. Nonetheless, LCR-related algorithms and tools have not gained wide appreciation across the research community, partly due to the fact that only a handful of user-friendly software is currently freely available. We developed LCR-eXXXplorer, an extensible online platform attempting to fill this gap. LCR-eXXXplorer offers tools for displaying LCRs from the UniProt/SwissProt knowledgebase, in combination with other relevant protein features, predicted or experimentally verified. Moreover, users may perform powerful queries against a custom designed sequence/LCR-centric database. We anticipate that LCR-eXXXplorer will be a useful starting point in research efforts for the elucidation of the structure, function and evolution of proteins with LCRs. LCR-eXXXplorer is freely available at the URL http://repeat.biol.ucy.ac.cy/lcr-exxxplorer. vprobon@ucy.ac.cy Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Interventions to Improve Hand Hygiene Compliance in the ICU: A Systematic Review.

PubMed

Lydon, Sinéad; Power, Michael; McSharry, Jennifer; Byrne, Molly; Madden, Caoimhe; Squires, Janet Elaine; O'Connor, Paul

2017-11-01

To synthesize the literature describing interventions to improve hand hygiene in ICUs, to evaluate the quality of the extant research, and to outline the type, and efficacy, of interventions described. Systematic searches were conducted in November 2016 using five electronic databases: Medline, CINAHL, PsycInfo, Embase, and Web of Science. Additionally, the reference lists of included studies and existing review papers were screened. English language, peer-reviewed studies that evaluated an intervention to improve hand hygiene in an adult ICU setting, and reported hand hygiene compliance rates collected via observation, were included. Data were extracted on the setting, participant characteristics, experimental design, hand hygiene measurement, intervention characteristics, and outcomes. Interventional components were categorized using the Behavior Change Wheel. Methodological quality was examined using the Downs and Black Checklist. Thirty-eight studies were included. The methodological quality of studies was poor, with studies scoring a mean of 8.6 of 24 (SD= 2.7). Over 90% of studies implemented a bundled intervention. The most frequently employed interventional strategies were education (78.9%), enablement (71.1%), training (68.4%), environmental restructuring (65.8%), and persuasion (65.8%). Intervention outcomes were variable, with a mean relative percentage change of 94.7% (SD= 195.7; range, 4.3-1155.4%) from pre to post intervention. This review demonstrates that best practice for improving hand hygiene in ICUs remains unestablished. Future research employing rigorous experimental designs, careful statistical analysis, and clearly described interventions is important.

National Rehabilitation Information Center

MedlinePlus

... search the NARIC website or one of our databases Select a database or search for a webpage A NARIC webpage ... Projects conducting research and/or development (NIDILRR Program Database). Organizations, agencies, and online resources that support people ...

Quantum search of a real unstructured database

NASA Astrophysics Data System (ADS)

Broda, Bogusław

2016-02-01

A simple circuit implementation of the oracle for Grover's quantum search of a real unstructured classical database is proposed. The oracle contains a kind of quantumly accessible classical memory, which stores the database.

Overcoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS)*

PubMed Central

Renard, Bernhard Y.; Xu, Buote; Kirchner, Marc; Zickmann, Franziska; Winter, Dominic; Korten, Simone; Brattig, Norbert W.; Tzur, Amit; Hamprecht, Fred A.; Steen, Hanno

2012-01-01

Currently, the reliable identification of peptides and proteins is only feasible when thoroughly annotated sequence databases are available. Although sequencing capacities continue to grow, many organisms remain without reliable, fully annotated reference genomes required for proteomic analyses. Standard database search algorithms fail to identify peptides that are not exactly contained in a protein database. De novo searches are generally hindered by their restricted reliability, and current error-tolerant search strategies are limited by global, heuristic tradeoffs between database and spectral information. We propose a Bayesian information criterion-driven error-tolerant peptide search (BICEPS) and offer an open source implementation based on this statistical criterion to automatically balance the information of each single spectrum and the database, while limiting the run time. We show that BICEPS performs as well as current database search algorithms when such algorithms are applied to sequenced organisms, whereas BICEPS only uses a remotely related organism database. For instance, we use a chicken instead of a human database corresponding to an evolutionary distance of more than 300 million years (International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716). We demonstrate the successful application to cross-species proteomics with a 33% increase in the number of identified proteins for a filarial nematode sample of Litomosoides sigmodontis. PMID:22493179

LigandBox: A database for 3D structures of chemical compounds

PubMed Central

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

LigandBox: A database for 3D structures of chemical compounds.

PubMed

Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

2013-01-01

A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

The MAO NASU Plate Archive Database. Current Status and Perspectives

NASA Astrophysics Data System (ADS)

Pakuliak, L. K.; Sergeeva, T. P.

2006-04-01

The preliminary online version of the database of the MAO NASU plate archive is constructed on the basis of the relational database management system MySQL and permits an easy supplement of database with new collections of astronegatives, provides a high flexibility in constructing SQL-queries for data search optimization, PHP Basic Authorization protected access to administrative interface and wide range of search parameters. The current status of the database will be reported and the brief description of the search engine and means of the database integrity support will be given. Methods and means of the data verification and tasks for the further development will be discussed.

Image database for digital hand atlas

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente; Dey, Partha S.; Gertych, Arkadiusz; Pospiech-Kurkowska, Sywia

2003-05-01

Bone age assessment is a procedure frequently performed in pediatric patients to evaluate their growth disorder. A commonly used method is atlas matching by a visual comparison of a hand radiograph with a small reference set of old Greulich-Pyle atlas. We have developed a new digital hand atlas with a large set of clinically normal hand images of diverse ethnic groups. In this paper, we will present our system design and implementation of the digital atlas database to support the computer-aided atlas matching for bone age assessment. The system consists of a hand atlas image database, a computer-aided diagnostic (CAD) software module for image processing and atlas matching, and a Web user interface. Users can use a Web browser to push DICOM images, directly or indirectly from PACS, to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, are then extracted and compared with patterns from the atlas image database to assess the bone age. The digital atlas method built on a large image database and current Internet technology provides an alternative to supplement or replace the traditional one for a quantitative, accurate and cost-effective assessment of bone age.

Adaptation of Decoy Fusion Strategy for Existing Multi-Stage Search Workflows

NASA Astrophysics Data System (ADS)

Ivanov, Mark V.; Levitsky, Lev I.; Gorshkov, Mikhail V.

2016-09-01

A number of proteomic database search engines implement multi-stage strategies aiming at increasing the sensitivity of proteome analysis. These approaches often employ a subset of the original database for the secondary stage of analysis. However, if target-decoy approach (TDA) is used for false discovery rate (FDR) estimation, the multi-stage strategies may violate the underlying assumption of TDA that false matches are distributed uniformly across the target and decoy databases. This violation occurs if the numbers of target and decoy proteins selected for the second search are not equal. Here, we propose a method of decoy database generation based on the previously reported decoy fusion strategy. This method allows unbiased TDA-based FDR estimation in multi-stage searches and can be easily integrated into existing workflows utilizing popular search engines and post-search algorithms.

Searching for evidence or approval? A commentary on database search in systematic reviews and alternative information retrieval methodologies.

PubMed

Delaney, Aogán; Tamás, Peter A

2018-03-01

Despite recognition that database search alone is inadequate even within the health sciences, it appears that reviewers in fields that have adopted systematic review are choosing to rely primarily, or only, on database search for information retrieval. This commentary reminds readers of factors that call into question the appropriateness of default reliance on database searches particularly as systematic review is adapted for use in new and lower consensus fields. It then discusses alternative methods for information retrieval that require development, formalisation, and evaluation. Our goals are to encourage reviewers to reflect critically and transparently on their choice of information retrieval methods and to encourage investment in research on alternatives. Copyright © 2017 John Wiley & Sons, Ltd.

Federated or cached searches: Providing expected performance from multiple invasive species databases

NASA Astrophysics Data System (ADS)

Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

2011-06-01

Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search "deep" web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

Federated or cached searches: providing expected performance from multiple invasive species databases

USGS Publications Warehouse

Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

2011-01-01

Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search “deep” web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

MICA: desktop software for comprehensive searching of DNA databases

PubMed Central

Stokes, William A; Glick, Benjamin S

2006-01-01

Background Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays) that allows large DNA databases to be searched efficiently using very little memory. Results MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. Conclusion MICA is suitable as a search engine for desktop DNA analysis software. PMID:17018144

Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules—Search Options and Applications in Food Science

PubMed Central

Minkiewicz, Piotr; Darewicz, Małgorzata; Iwaniak, Anna; Bucholska, Justyna; Starowicz, Piotr; Czyrko, Emilia

2016-01-01

Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components) and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs. PMID:27929431

Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science.

PubMed

Minkiewicz, Piotr; Darewicz, Małgorzata; Iwaniak, Anna; Bucholska, Justyna; Starowicz, Piotr; Czyrko, Emilia

2016-12-06

Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components) and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs.

Absence of carious lesions at margins of glass-ionomer cement and amalgam restorations: An update of systematic review evidence

PubMed Central

2011-01-01

Background This article aims to update the existing systematic review evidence elicited by Mickenautsch et al. up to 18 January 2008 (published in the European Journal of Paediatric Dentistry in 2009) and addressing the review question of whether, in the same dentition and same cavity class, glass-ionomer cement (GIC) restored cavities show less recurrent carious lesions on cavity margins than cavities restored with amalgam. Methods The systematic literature search was extended beyond the original search date and a further hand-search and reference check was done. The quality of accepted trials was assessed, using updated quality criteria, and the risk of bias was investigated in more depth than previously reported. In addition, the focus of quantitative synthesis was shifted to single datasets extracted from the accepted trials. Results The database search (up to 10 August 2010) identified 1 new trial, in addition to the 9 included in the original systematic review, and 11 further trials were included after a hand-search and reference check. Of these 21 trials, 11 were excluded and 10 were accepted for data extraction and quality assessment. Thirteen dichotomous datasets of primary outcomes and 4 datasets with secondary outcomes were extracted. Meta-analysis and cumulative meta-analysis were used in combining clinically homogenous datasets. The overall results of the computed datasets suggest that GIC has a higher caries-preventive effect than amalgam for restorations in permanent teeth. No difference was found for restorations in the primary dentition. Conclusion This outcome is in agreement with the conclusions of the original systematic review. Although the findings of the trials identified in this update may be considered to be less affected by attrition- and publication bias, their risk of selection- and detection/performance bias is high. Thus, verification of the currently available results requires further high-quality randomised control trials. PMID:21396097

Searching for Controlled Trials of Complementary and Alternative Medicine: A Comparison of 15 Databases

PubMed Central

Cogo, Elise; Sampson, Margaret; Ajiferuke, Isola; Manheimer, Eric; Campbell, Kaitryn; Daniel, Raymond; Moher, David

2011-01-01

This project aims to assess the utility of bibliographic databases beyond the three major ones (MEDLINE, EMBASE and Cochrane CENTRAL) for finding controlled trials of complementary and alternative medicine (CAM). Fifteen databases were searched to identify controlled clinical trials (CCTs) of CAM not also indexed in MEDLINE. Searches were conducted in May 2006 using the revised Cochrane highly sensitive search strategy (HSSS) and the PubMed CAM Subset. Yield of CAM trials per 100 records was determined, and databases were compared over a standardized period (2005). The Acudoc2 RCT, Acubriefs, Index to Chiropractic Literature (ICL) and Hom-Inform databases had the highest concentrations of non-MEDLINE records, with more than 100 non-MEDLINE records per 500. Other productive databases had ratios between 500 and 1500 records to 100 non-MEDLINE records—these were AMED, MANTIS, PsycINFO, CINAHL, Global Health and Alt HealthWatch. Five databases were found to be unproductive: AGRICOLA, CAIRSS, Datadiwan, Herb Research Foundation and IBIDS. Acudoc2 RCT yielded 100 CAM trials in the most recent 100 records screened. Acubriefs, AMED, Hom-Inform, MANTIS, PsycINFO and CINAHL had more than 25 CAM trials per 100 records screened. Global Health, ICL and Alt HealthWatch were below 25 in yield. There were 255 non-MEDLINE trials from eight databases in 2005, with only 10% indexed in more than one database. Yield varied greatly between databases; the most productive databases from both sampling methods were Acubriefs, Acudoc2 RCT, AMED and CINAHL. Low overlap between databases indicates comprehensive CAM literature searches will require multiple databases. PMID:19468052

Searching for controlled trials of complementary and alternative medicine: a comparison of 15 databases.

PubMed

Cogo, Elise; Sampson, Margaret; Ajiferuke, Isola; Manheimer, Eric; Campbell, Kaitryn; Daniel, Raymond; Moher, David

2011-01-01

This project aims to assess the utility of bibliographic databases beyond the three major ones (MEDLINE, EMBASE and Cochrane CENTRAL) for finding controlled trials of complementary and alternative medicine (CAM). Fifteen databases were searched to identify controlled clinical trials (CCTs) of CAM not also indexed in MEDLINE. Searches were conducted in May 2006 using the revised Cochrane highly sensitive search strategy (HSSS) and the PubMed CAM Subset. Yield of CAM trials per 100 records was determined, and databases were compared over a standardized period (2005). The Acudoc2 RCT, Acubriefs, Index to Chiropractic Literature (ICL) and Hom-Inform databases had the highest concentrations of non-MEDLINE records, with more than 100 non-MEDLINE records per 500. Other productive databases had ratios between 500 and 1500 records to 100 non-MEDLINE records-these were AMED, MANTIS, PsycINFO, CINAHL, Global Health and Alt HealthWatch. Five databases were found to be unproductive: AGRICOLA, CAIRSS, Datadiwan, Herb Research Foundation and IBIDS. Acudoc2 RCT yielded 100 CAM trials in the most recent 100 records screened. Acubriefs, AMED, Hom-Inform, MANTIS, PsycINFO and CINAHL had more than 25 CAM trials per 100 records screened. Global Health, ICL and Alt HealthWatch were below 25 in yield. There were 255 non-MEDLINE trials from eight databases in 2005, with only 10% indexed in more than one database. Yield varied greatly between databases; the most productive databases from both sampling methods were Acubriefs, Acudoc2 RCT, AMED and CINAHL. Low overlap between databases indicates comprehensive CAM literature searches will require multiple databases.

End User Information Searching on the Internet: How Do Users Search and What Do They Search For? (SIG USE)

ERIC Educational Resources Information Center

Saracevic, Tefko

2000-01-01

Summarizes a presentation that discussed findings and implications of research projects using an Internet search service and Internet-accessible vendor databases, representing the two sides of public database searching: query formulation and resource utilization. Presenters included: Tefko Saracevic, Amanda Spink, Dietmar Wolfram and Hong Xie.…

Assessment of Metabolome Annotation Quality: A Method for Evaluating the False Discovery Rate of Elemental Composition Searches

PubMed Central

Matsuda, Fumio; Shinbo, Yoko; Oikawa, Akira; Hirai, Masami Yokota; Fiehn, Oliver; Kanaya, Shigehiko; Saito, Kazuki

2009-01-01

Background In metabolomics researches using mass spectrometry (MS), systematic searching of high-resolution mass data against compound databases is often the first step of metabolite annotation to determine elemental compositions possessing similar theoretical mass numbers. However, incorrect hits derived from errors in mass analyses will be included in the results of elemental composition searches. To assess the quality of peak annotation information, a novel methodology for false discovery rates (FDR) evaluation is presented in this study. Based on the FDR analyses, several aspects of an elemental composition search, including setting a threshold, estimating FDR, and the types of elemental composition databases most reliable for searching are discussed. Methodology/Principal Findings The FDR can be determined from one measured value (i.e., the hit rate for search queries) and four parameters determined by Monte Carlo simulation. The results indicate that relatively high FDR values (30–50%) were obtained when searching time-of-flight (TOF)/MS data using the KNApSAcK and KEGG databases. In addition, searches against large all-in-one databases (e.g., PubChem) always produced unacceptable results (FDR >70%). The estimated FDRs suggest that the quality of search results can be improved not only by performing more accurate mass analysis but also by modifying the properties of the compound database. A theoretical analysis indicates that FDR could be improved by using compound database with smaller but higher completeness entries. Conclusions/Significance High accuracy mass analysis, such as Fourier transform (FT)-MS, is needed for reliable annotation (FDR <10%). In addition, a small, customized compound database is preferable for high-quality annotation of metabolome data. PMID:19847304

NREL: Renewable Resource Data Center - Biomass Resource Publications

Science.gov Websites

Marginal Lands in APEC Economies NREL Publications Database For a comprehensive list of other NREL biomass resource publications, explore NREL's Publications Database. When searching the database, search on "

Hand hygiene to reduce community transmission of influenza and acute respiratory tract infection: a systematic review.

PubMed

Warren-Gash, Charlotte; Fragaszy, Ellen; Hayward, Andrew C

2013-09-01

Hand hygiene may be associated with modest protection against some acute respiratory tract infections, but its specific role in influenza transmission in different settings is unclear. We aimed to review evidence that improving hand hygiene reduces primary and secondary transmission of (i) influenza and (ii) acute respiratory tract infections in community settings. We searched Medline, Embase, Global Health and Cochrane databases up to 13 February 2012 for reports in any language of original research investigating the effect of hand hygiene on influenza or acute respiratory tract infection where aetiology was unspecified in community settings including institutions such as schools, and domestic residences. Data were presented and quality rated across outcomes according to the Grading of Recommendations Assessment, Development and Evaluation system. Sixteen articles met inclusion criteria. There was moderate to low-quality evidence of a reduction in both influenza and respiratory tract infection with hand hygiene interventions in schools, greatest in a lower-middle-income setting. There was high-quality evidence of a small reduction in respiratory infection in childcare settings. There was high-quality evidence for a large reduction in respiratory infection with a hand hygiene intervention in squatter settlements in a low-income setting. There was moderate- to high-quality evidence of no effect on secondary transmission of influenza in households that had already experienced an index case. While hand hygiene interventions have potential to reduce transmission of influenza and acute respiratory tract infections, their effectiveness varies depending on setting, context and compliance. © 2012 John Wiley & Sons Ltd.

A review on the application of medical infrared thermal imaging in hands

NASA Astrophysics Data System (ADS)

Sousa, Elsa; Vardasca, Ricardo; Teixeira, Sérgio; Seixas, Adérito; Mendes, Joaquim; Costa-Ferreira, António

2017-09-01

Infrared Thermal (IRT) imaging is a medical imaging modality to study skin temperature in real time, providing physiological information about the underlining structures. One of the most accessible body sites to be investigated using such imaging method is the hands, which can reflect valuable information about conditions affecting the upper limbs. The aim of this review is to acquaint the successful applications of IRT in the hands with a medical scope, opening horizons for future applications based in the achieved results. A systematic literature review was performed in order to assess in which applications medical IRT imaging was applied to the hands. The literature search was conducted in the reference databases: PubMed, Scopus and ISI Web of Science, making use of keywords (hand, thermography, infrared imaging, thermal imaging) combination that were present at the title and abstract. No temporal restriction was made. As a result, 4260 articles were identified, after removal of duplicates, 3224 articles remained and from first title and abstract filtering, a total of 388 articles were considered. After application of exclusion criteria (non-availability, non-clinical applications, reviews, case studies, written in other languages than English and using liquid crystal thermography), 146 articles were considered for this review. It can be verified that thermography provides useful diagnostic and monitoring information of conditions that directly or indirectly related to hands, as well as aiding in the treatment assessment. Trends and future challenges for IRT applications on hands are provided to stimulate researchers and clinicians to explore and address them.

Should we search Chinese biomedical databases when performing systematic reviews?

PubMed

Cohen, Jérémie F; Korevaar, Daniël A; Wang, Junfeng; Spijker, René; Bossuyt, Patrick M

2015-03-06

Chinese biomedical databases contain a large number of publications available to systematic reviewers, but it is unclear whether they are used for synthesizing the available evidence. We report a case of two systematic reviews on the accuracy of anti-cyclic citrullinated peptide for diagnosing rheumatoid arthritis. In one of these, the authors did not search Chinese databases; in the other, they did. We additionally assessed the extent to which Cochrane reviewers have searched Chinese databases in a systematic overview of the Cochrane Library (inception to 2014). The two diagnostic reviews included a total of 269 unique studies, but only 4 studies were included in both reviews. The first review included five studies published in the Chinese language (out of 151) while the second included 114 (out of 118). The summary accuracy estimates from the two reviews were comparable. Only 243 of the published 8,680 Cochrane reviews (less than 3%) searched one or more of the five major Chinese databases. These Chinese databases index about 2,500 journals, of which less than 6% are also indexed in MEDLINE. All 243 Cochrane reviews evaluated an intervention, 179 (74%) had at least one author with a Chinese affiliation; 118 (49%) addressed a topic in complementary or alternative medicine. Although searching Chinese databases may lead to the identification of a large amount of additional clinical evidence, Cochrane reviewers have rarely included them in their search strategy. We encourage future initiatives to evaluate more systematically the relevance of searching Chinese databases, as well as collaborative efforts to allow better incorporation of Chinese resources in systematic reviews.

NBIC: Search Ballast Report Database

Science.gov Websites

Smithsonian Environmental Research Center Logo US Coast Guard Logo Submit BW Report | Search NBIC Database developed an online database that can be queried through our website. Data are accessible for all coastal Lakes, have been incorporated into the NBIC database as of August 2004. Information on data availability

Ocean Drilling Program: Science Operator Search Engine

Science.gov Websites

and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main -USIO site, plus IODP, ODP, and DSDP Publications, together or separately. ODP | Search | Database

Using the TIGR gene index databases for biological discovery.

PubMed

Lee, Yuandan; Quackenbush, John

2003-11-01

The TIGR Gene Index web pages provide access to analyses of ESTs and gene sequences for nearly 60 species, as well as a number of resources derived from these. Each species-specific database is presented using a common format with a homepage. A variety of methods exist that allow users to search each species-specific database. Methods implemented currently include nucleotide or protein sequence queries using WU-BLAST, text-based searches using various sequence identifiers, searches by gene, tissue and library name, and searches using functional classes through Gene Ontology assignments. This protocol provides guidance for using the Gene Index Databases to extract information.

HER-2 expression in biopsy and surgical specimen on prognosis of osteosarcoma: A systematic review and meta-analysis of 16 studies.

PubMed

Zhang, Qingyu; Liu, Fanxiao; Wang, Bomin; Li, Zhenfeng; Zhou, Dongsheng; Yang, Qiang; Dong, Jinlei; Li, Jianmin

2016-06-01

Numerous original clinical studies have attempted to investigate the prognostic value of HER-2 overexpression in osteosarcoma, but the results of these studies are not consistent. This meta-analysis and systematic review was performed to further assess the correlation between HER-2 expression and prognosis in patients with osteosarcoma. A detailed search of relevant publications was conducted using 7 electronic databases: PubMed, Embase, the Cochrane library, the Wanfang database, the China National Knowledge Internet (CNKI) database, the Chinese VIP database, and the Chinese Biological Medical (CBM) Database for publications through August 1, 2015, using the following keywords (HER-2 OR ErbB-2 OR C-erbB-2 OR neu) AND (osteosarcoma OR osteogenic tumor). The bibliographies of potentially relevant articles and identified articles were then searched by hand. Eligible studies were those that enrolled participants with osteosarcoma and provided survival outcome in HER-2 positive and negative groups. The hazard ratio (HR) and 95% confidence interval (CI) for each individual study was calculated and pooled to obtain integrated estimates, using random effects modeling. Sixteen studies involving 934 participants with osteosarcoma met our inclusion criteria. HER-2 overexpression was documented in 42.2% of patients with osteosarcoma. Compared with patients without HER-2 overexpression, those overexpressing HER-2 had decreased overall survival (HR = 2.03, 95% CI: 1.36-3.03, P < 0.001). Statistical associations between HER-2 overexpression and unfavorable overall survival (OS) were observed for both biopsy and surgical removal specimens (HR = 2.07, 95%CI: 1.16-3.72, P = 0.014; and HR = 2.02, 95%CI: 1.10-3.71, P = 0.024). Results for disease-free survival (DFS) were similar. Overexpression of HER-2 is significantly associated with poor outcome for patients with osteosarcoma and should be assessed at diagnosis and after surgery as a prognostic factor. However, larger-scale multicenter clinical studies are needed to further support these findings.

An Online Resource for Flight Test Safety Planning

NASA Technical Reports Server (NTRS)

Lewis, Greg

2007-01-01

A viewgraph presentation describing an online database for flight test safety techniques is shown. The topics include: 1) Goal; 2) Test Hazard Analyses; 3) Online Database Background; 4) Data Gathering; 5) NTPS Role; 6) Organizations; 7) Hazard Titles; 8) FAR Paragraphs; 9) Maneuver Name; 10) Identified Hazard; 11) Matured Hazard Titles; 12) Loss of Control Causes; 13) Mitigations; 14) Database Now Open to the Public; 15) FAR Reference Search; 16) Record Field Search; 17) Keyword Search; and 18) Results of FAR Reference Search.

Searching Databases without Query-Building Aids: Implications for Dyslexic Users

ERIC Educational Resources Information Center

Berget, Gerd; Sandnes, Frode Eika

2015-01-01

Introduction: Few studies document the information searching behaviour of users with cognitive impairments. This paper therefore addresses the effect of dyslexia on information searching in a database with no tolerance for spelling errors and no query-building aids. The purpose was to identify effective search interface design guidelines that…

Conducting a Web Search.

ERIC Educational Resources Information Center

Miller-Whitehead, Marie

Keyword and text string searches of online library catalogs often provide different results according to library and database used and depending upon how books and journals are indexed. For this reason, online databases such as ERIC often provide tutorials and recommendations for searching their site, such as how to use Boolean search strategies.…

Citation searching: a systematic review case study of multiple risk behaviour interventions

PubMed Central

2014-01-01

Background The value of citation searches as part of the systematic review process is currently unknown. While the major guides to conducting systematic reviews state that citation searching should be carried out in addition to searching bibliographic databases there are still few studies in the literature that support this view. Rather than using a predefined search strategy to retrieve studies, citation searching uses known relevant papers to identify further papers. Methods We describe a case study about the effectiveness of using the citation sources Google Scholar, Scopus, Web of Science and OVIDSP MEDLINE to identify records for inclusion in a systematic review. We used the 40 included studies identified by traditional database searches from one systematic review of interventions for multiple risk behaviours. We searched for each of the included studies in the four citation sources to retrieve the details of all papers that have cited these studies. We carried out two analyses; the first was to examine the overlap between the four citation sources to identify which citation tool was the most useful; the second was to investigate whether the citation searches identified any relevant records in addition to those retrieved by the original database searches. Results The highest number of citations was retrieved from Google Scholar (1680), followed by Scopus (1173), then Web of Science (1095) and lastly OVIDSP (213). To retrieve all the records identified by the citation tracking searching all four resources was required. Google Scholar identified the highest number of unique citations. The citation tracking identified 9 studies that met the review’s inclusion criteria. Eight of these had already been identified by the traditional databases searches and identified in the screening process while the ninth was not available in any of the databases when the original searches were carried out. It would, however, have been identified by two of the database search strategies if searches had been carried out later. Conclusions Based on the results from this investigation, citation searching as a supplementary search method for systematic reviews may not be the best use of valuable time and resources. It would be useful to verify these findings in other reviews. PMID:24893958

BEAUTY-X: enhanced BLAST searches for DNA queries.

PubMed

Worley, K C; Culpepper, P; Wiese, B A; Smith, R F

1998-01-01

BEAUTY (BLAST Enhanced Alignment Utility) is an enhanced version of the BLAST database search tool that facilitates identification of the functions of matched sequences. Three recent improvements to the BEAUTY program described here make the enhanced output (1) available for DNA queries, (2) available for searches of any protein database, and (3) more up-to-date, with periodic updates of the domain information. BEAUTY searches of the NCBI and EMBL non-redundant protein sequence databases are available from the BCM Search Launcher Web pages (http://gc.bcm.tmc. edu:8088/search-launcher/launcher.html). BEAUTY Post-Processing of submitted search results is available using the BCM Search Launcher Batch Client (version 2.6) (ftp://gc.bcm.tmc. edu/pub/software/search-launcher/). Example figures are available at http://dot.bcm.tmc. edu:9331/papers/beautypp.html (kworley,culpep)@bcm.tmc.edu

Experiences in the creation of an electromyography database to help hand amputated persons.

PubMed

Atzori, Manfredo; Gijsberts, Arjan; Heynen, Simone; Hager, Anne-Gabrielle Mittaz; Castellimi, Claudio; Caputo, Barbara; Müller, Henning

2012-01-01

Currently, trans-radial amputees can only perform a few simple movements with prosthetic hands. This is mainly due to low control capabilities and the long training time that is required to learn controlling them with surface electromyography (sEMG). This is in contrast with recent advances in mechatronics, thanks to which mechanical hands have multiple degrees of freedom and in some cases force control. To help improve the situation, we are building the NinaPro (Non-Invasive Adaptive Prosthetics) database, a database of about 50 hand and wrist movements recorded from several healthy and currently very few amputated persons that will help the community to test and improve sEMG-based natural control systems for prosthetic hands. In this paper we describe the experimental experiences and practical aspects related to the data acquisition.

Banked preterm versus banked term human milk to promote growth and development in very low birth weight infants.

PubMed

Dempsey, Eugene; Miletin, Jan

2010-06-16

Human milk banking has been available in many countries for the last three decades. The milk provided from milk banking is predominantly term breast milk, but some milk banks provide preterm breast milk. There are a number of differences between donor term and donor preterm human milk. To determine the effect of banked preterm milk compared with banked term milk regarding growth and developmental outcome in very low birth weight infants (infants weighing less than 1500 g). We used the standard methods of the Cochrane Neonatal Review Group, including a search of the Cochrane Neonatal Group specialized register and the Cochrane Central Register of Controlled Trials (CENTRAL, The Cochrane Library, January 2010). We searched the computerised bibliographic databases MEDLINE (1966 to February 2010), EMBASE (1988 to February 2010) and Web of Science (1975 to February 2010). We searched reference lists of all selected articles, review articles and the Oxford Database of Perinatal Trials. We also searched abstracts from neonatal and pediatric meetings (PAS electronic version from 2000 to 2009, ESPR hand search from 2000 to 2009). We applied no language restrictions. Randomised and quasi-randomised trials comparing banked donor preterm milk with banked donor term milk regarding growth and developmental outcomes in very low birth weight infants We planned to perform assessment of methodology regarding blinding of randomisation, intervention and outcome measurements as well as completeness of follow-up. We planned to evaluate treatment effect using a fixed-effect model using relative risk (RR), relative risk reduction, risk difference (RD) and number needed to treat (NNT) for categorical data and using mean, standard deviation and weighted mean difference (WMD) for continuous data. We planned an evaluation of heterogeneity. No studies met the inclusion criteria. There are no randomised trials that compare preterm banked milk to banked term milk to promote growth and development in very low birth weight infants.

Digital hand atlas and computer-aided bone age assessment via the Web

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente

1999-07-01

A frequently used assessment method of bone age is atlas matching by a radiological examination of a hand image against a reference set of atlas patterns of normal standards. We are in a process of developing a digital hand atlas with a large standard set of normal hand and wrist images that reflect the skeletal maturity, race and sex difference, and current child development. The digital hand atlas will be used for a computer-aided bone age assessment via Web. We have designed and partially implemented a computer-aided diagnostic (CAD) system for Web-based bone age assessment. The system consists of a digital hand atlas, a relational image database and a Web-based user interface. The digital atlas is based on a large standard set of normal hand an wrist images with extracted bone objects and quantitative features. The image database uses a content- based indexing to organize the hand images and their attributes and present to users in a structured way. The Web-based user interface allows users to interact with the hand image database from browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, will be extracted and compared with patterns from the atlas database to assess the bone age. The relevant reference imags and the final assessment report will be sent back to the user's browser via Web. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. In this paper, we present the system design and Web-based client-server model for computer-assisted bone age assessment and our initial implementation of the digital atlas database.

A comparative study of six European databases of medically oriented Web resources.

PubMed

Abad García, Francisca; González Teruel, Aurora; Bayo Calduch, Patricia; de Ramón Frias, Rosa; Castillo Blasco, Lourdes

2005-10-01

The paper describes six European medically oriented databases of Web resources, pertaining to five quality-controlled subject gateways, and compares their performance. The characteristics, coverage, procedure for selecting Web resources, record structure, searching possibilities, and existence of user assistance were described for each database. Performance indicators for each database were obtained by means of searches carried out using the key words, "myocardial infarction." Most of the databases originated in the 1990s in an academic or library context and include all types of Web resources of an international nature. Five databases use Medical Subject Headings. The number of fields per record varies between three and nineteen. The language of the search interfaces is mostly English, and some of them allow searches in other languages. In some databases, the search can be extended to Pubmed. Organizing Medical Networked Information, Catalogue et Index des Sites Médicaux Francophones, and Diseases, Disorders and Related Topics produced the best results. The usefulness of these databases as quick reference resources is clear. In addition, their lack of content overlap means that, for the user, they complement each other. Their continued survival faces three challenges: the instability of the Internet, maintenance costs, and lack of use in spite of their potential usefulness.

Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows.

PubMed

Verheggen, Kenneth; Raeder, Helge; Berven, Frode S; Martens, Lennart; Barsnes, Harald; Vaudel, Marc

2017-09-13

Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we present the common paradigm behind the different implementations, and its limitations for modern mass spectrometry datasets. We also detail how the search engines attempt to alleviate these limitations, and provide an overview of the different software frameworks available to the researcher. Finally, we highlight alternative approaches for the identification of proteomic mass spectrometry datasets, either as a replacement for, or as a complement to, sequence database search engines. © 2017 Wiley Periodicals, Inc.

Validity of International Classification of Diseases (ICD) coding for dengue infections in hospital discharge records in Malaysia.

PubMed

Woon, Yuan-Liang; Lee, Keng-Yee; Mohd Anuar, Siti Fatimah Zahra; Goh, Pik-Pin; Lim, Teck-Onn

2018-04-20

Hospitalization due to dengue illness is an important measure of dengue morbidity. However, limited studies are based on administrative database because the validity of the diagnosis codes is unknown. We validated the International Classification of Diseases, 10th revision (ICD) diagnosis coding for dengue infections in the Malaysian Ministry of Health's (MOH) hospital discharge database. This validation study involves retrospective review of available hospital discharge records and hand-search medical records for years 2010 and 2013. We randomly selected 3219 hospital discharge records coded with dengue and non-dengue infections as their discharge diagnoses from the national hospital discharge database. We then randomly sampled 216 and 144 records for patients with and without codes for dengue respectively, in keeping with their relative frequency in the MOH database, for chart review. The ICD codes for dengue were validated against lab-based diagnostic standard (NS1 or IgM). The ICD-10-CM codes for dengue had a sensitivity of 94%, modest specificity of 83%, positive predictive value of 87% and negative predictive value 92%. These results were stable between 2010 and 2013. However, its specificity decreased substantially when patients manifested with bleeding or low platelet count. The diagnostic performance of the ICD codes for dengue in the MOH's hospital discharge database is adequate for use in health services research on dengue.

Privacy-preserving search for chemical compound databases.

PubMed

Shimizu, Kana; Nuida, Koji; Arai, Hiromi; Mitsunari, Shigeo; Attrapadung, Nuttapong; Hamada, Michiaki; Tsuda, Koji; Hirokawa, Takatsugu; Sakuma, Jun; Hanaoka, Goichiro; Asai, Kiyoshi

2015-01-01

Searching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid of the query being monitored by the database server, usually downloads all the records in the database and uses them in a closed network. However, a serious dilemma arises when the database holder also wants to output no information except for the search results, and such a dilemma prevents the use of many important data resources. In order to overcome this dilemma, we developed a novel cryptographic protocol that enables database searching while keeping both the query holder's privacy and database holder's privacy. Generally, the application of cryptographic techniques to practical problems is difficult because versatile techniques are computationally expensive while computationally inexpensive techniques can perform only trivial computation tasks. In this study, our protocol is successfully built only from an additive-homomorphic cryptosystem, which allows only addition performed on encrypted values but is computationally efficient compared with versatile techniques such as general purpose multi-party computation. In an experiment searching ChEMBL, which consists of more than 1,200,000 compounds, the proposed method was 36,900 times faster in CPU time and 12,000 times as efficient in communication size compared with general purpose multi-party computation. We proposed a novel privacy-preserving protocol for searching chemical compound databases. The proposed method, easily scaling for large-scale databases, may help to accelerate drug discovery research by making full use of unused but valuable data that includes sensitive information.

Privacy-preserving search for chemical compound databases

PubMed Central

2015-01-01

Background Searching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid of the query being monitored by the database server, usually downloads all the records in the database and uses them in a closed network. However, a serious dilemma arises when the database holder also wants to output no information except for the search results, and such a dilemma prevents the use of many important data resources. Results In order to overcome this dilemma, we developed a novel cryptographic protocol that enables database searching while keeping both the query holder's privacy and database holder's privacy. Generally, the application of cryptographic techniques to practical problems is difficult because versatile techniques are computationally expensive while computationally inexpensive techniques can perform only trivial computation tasks. In this study, our protocol is successfully built only from an additive-homomorphic cryptosystem, which allows only addition performed on encrypted values but is computationally efficient compared with versatile techniques such as general purpose multi-party computation. In an experiment searching ChEMBL, which consists of more than 1,200,000 compounds, the proposed method was 36,900 times faster in CPU time and 12,000 times as efficient in communication size compared with general purpose multi-party computation. Conclusion We proposed a novel privacy-preserving protocol for searching chemical compound databases. The proposed method, easily scaling for large-scale databases, may help to accelerate drug discovery research by making full use of unused but valuable data that includes sensitive information. PMID:26678650

Global search tool for the Advanced Photon Source Integrated Relational Model of Installed Systems (IRMIS) database.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quock, D. E. R.; Cianciarulo, M. B.; APS Engineering Support Division

2007-01-01

The Integrated Relational Model of Installed Systems (IRMIS) is a relational database tool that has been implemented at the Advanced Photon Source to maintain an updated account of approximately 600 control system software applications, 400,000 process variables, and 30,000 control system hardware components. To effectively display this large amount of control system information to operators and engineers, IRMIS was initially built with nine Web-based viewers: Applications Organizing Index, IOC, PLC, Component Type, Installed Components, Network, Controls Spares, Process Variables, and Cables. However, since each viewer is designed to provide details from only one major category of the control system, themore » necessity for a one-stop global search tool for the entire database became apparent. The user requirements for extremely fast database search time and ease of navigation through search results led to the choice of Asynchronous JavaScript and XML (AJAX) technology in the implementation of the IRMIS global search tool. Unique features of the global search tool include a two-tier level of displayed search results, and a database data integrity validation and reporting mechanism.« less

[Profile of a systematic search. Search areas, databases and reports].

PubMed

Korsbek, Lisa; Bendix, Ane Friis; Kidholm, Kristian

2006-04-03

Systematic literature search is a fundamental in evidence-based medicine. But systematic literature search is not yet a very well used way of retrieving evidence-based information. This article profiles a systematic literature search for evidence-based literature. It goes through the most central databases and gives an example of how to document the literature search. The article also sums up the literature search in all reviews in Ugeskrift for Laeger in the year 2004.

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.

PubMed

Jagtap, Pratik; Goslinga, Jill; Kooren, Joel A; McGowan, Thomas; Wroblewski, Matthew S; Seymour, Sean L; Griffin, Timothy J

2013-04-01

Large databases (>10(6) sequences) used in metaproteomic and proteogenomic studies present challenges in matching peptide sequences to MS/MS data using database-search programs. Most notably, strict filtering to avoid false-positive matches leads to more false negatives, thus constraining the number of peptide matches. To address this challenge, we developed a two-step method wherein matches derived from a primary search against a large database were used to create a smaller subset database. The second search was performed against a target-decoy version of this subset database merged with a host database. High confidence peptide sequence matches were then used to infer protein identities. Applying our two-step method for both metaproteomic and proteogenomic analysis resulted in twice the number of high confidence peptide sequence matches in each case, as compared to the conventional one-step method. The two-step method captured almost all of the same peptides matched by the one-step method, with a majority of the additional matches being false negatives from the one-step method. Furthermore, the two-step method improved results regardless of the database search program used. Our results show that our two-step method maximizes the peptide matching sensitivity for applications requiring large databases, especially valuable for proteogenomics and metaproteomics studies. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hand hygiene to reduce community transmission of influenza and acute respiratory tract infection: a systematic review

PubMed Central

Warren‐Gash, Charlotte; Fragaszy, Ellen; Hayward, Andrew C.

2012-01-01

Please cite this paper as: Warren‐Gash et al. (2012) Hand hygiene to reduce community transmission of influenza and acute respiratory tract infection: a systematic review. Influenza and Other Respiratory Viruses DOI: 10.1111/irv.12015. Hand hygiene may be associated with modest protection against some acute respiratory tract infections, but its specific role in influenza transmission in different settings is unclear. We aimed to review evidence that improving hand hygiene reduces primary and secondary transmission of (i) influenza and (ii) acute respiratory tract infections in community settings. We searched Medline, Embase, Global Health and Cochrane databases up to 13 February 2012 for reports in any language of original research investigating the effect of hand hygiene on influenza or acute respiratory tract infection where aetiology was unspecified in community settings including institutions such as schools, and domestic residences. Data were presented and quality rated across outcomes according to the Grading of Recommendations Assessment, Development and Evaluation system. Sixteen articles met inclusion criteria. There was moderate to low‐quality evidence of a reduction in both influenza and respiratory tract infection with hand hygiene interventions in schools, greatest in a lower–middle‐income setting. There was high‐quality evidence of a small reduction in respiratory infection in childcare settings. There was high‐quality evidence for a large reduction in respiratory infection with a hand hygiene intervention in squatter settlements in a low‐income setting. There was moderate‐ to high‐quality evidence of no effect on secondary transmission of influenza in households that had already experienced an index case. While hand hygiene interventions have potential to reduce transmission of influenza and acute respiratory tract infections, their effectiveness varies depending on setting, context and compliance. PMID:23043518

University Faculty Use of Computerized Databases: An Assessment of Needs and Resources.

ERIC Educational Resources Information Center

Borgman, Christine L.; And Others

1985-01-01

Results of survey indicate that: academic faculty are unaware of range of databases available; few recognize need for databases in research; most delegate searching to librarian or assistant, rather than perform searching themselves; and 39 database guides identified tended to be descriptive rather than evaluative. A comparison of the guides is…

Sagace: A web-based search engine for biomedical databases in Japan

PubMed Central

2012-01-01

Background In the big data era, biomedical research continues to generate a large amount of data, and the generated information is often stored in a database and made publicly available. Although combining data from multiple databases should accelerate further studies, the current number of life sciences databases is too large to grasp features and contents of each database. Findings We have developed Sagace, a web-based search engine that enables users to retrieve information from a range of biological databases (such as gene expression profiles and proteomics data) and biological resource banks (such as mouse models of disease and cell lines). With Sagace, users can search more than 300 databases in Japan. Sagace offers features tailored to biomedical research, including manually tuned ranking, a faceted navigation to refine search results, and rich snippets constructed with retrieved metadata for each database entry. Conclusions Sagace will be valuable for experts who are involved in biomedical research and drug development in both academia and industry. Sagace is freely available at http://sagace.nibio.go.jp/en/. PMID:23110816

OrChem - An open source chemistry search engine for Oracle(R).

PubMed

Rijnbeek, Mark; Steinbeck, Christoph

2009-10-22

Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net.

Mass spectrometry-based protein identification by integrating de novo sequencing with database searching.

PubMed

Wang, Penghao; Wilson, Susan R

2013-01-01

Mass spectrometry-based protein identification is a very challenging task. The main identification approaches include de novo sequencing and database searching. Both approaches have shortcomings, so an integrative approach has been developed. The integrative approach firstly infers partial peptide sequences, known as tags, directly from tandem spectra through de novo sequencing, and then puts these sequences into a database search to see if a close peptide match can be found. However the current implementation of this integrative approach has several limitations. Firstly, simplistic de novo sequencing is applied and only very short sequence tags are used. Secondly, most integrative methods apply an algorithm similar to BLAST to search for exact sequence matches and do not accommodate sequence errors well. Thirdly, by applying these methods the integrated de novo sequencing makes a limited contribution to the scoring model which is still largely based on database searching. We have developed a new integrative protein identification method which can integrate de novo sequencing more efficiently into database searching. Evaluated on large real datasets, our method outperforms popular identification methods.

LMSD: LIPID MAPS structure database

PubMed Central

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Brown, Alex; Dennis, Edward A.; Glass, Christopher K.; Merrill, Alfred H.; Murphy, Robert C.; Raetz, Christian R. H.; Russell, David W.; Subramaniam, Shankar

2007-01-01

The LIPID MAPS Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. Structures of lipids in the database come from four sources: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) computationally generated structures for appropriate lipid classes; (iv) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT and other public sources. All the lipid structures in LMSD are drawn in a consistent fashion. In addition to a classification-based retrieval of lipids, users can search LMSD using either text-based or structure-based search options. The text-based search implementation supports data retrieval by any combination of these data fields: LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass data fields. The structure-based search, in conjunction with optional data fields, provides the capability to perform a substructure search or exact match for the structure drawn by the user. Search results, in addition to structure and annotations, also include relevant links to external databases. The LMSD is publicly available at PMID:17098933

Term Relevance Feedback and Mediated Database Searching: Implications for Information Retrieval Practice and Systems Design.

ERIC Educational Resources Information Center

Spink, Amanda

1995-01-01

This study uses the human approach to examine the sources and effectiveness of search terms selected during 40 mediated interactive database searches and focuses on determining the retrieval effectiveness of search terms identified by users and intermediaries from retrieved items during term relevance feedback. (Author/JKP)

The Weaknesses of Full-Text Searching

ERIC Educational Resources Information Center

Beall, Jeffrey

2008-01-01

This paper provides a theoretical critique of the deficiencies of full-text searching in academic library databases. Because full-text searching relies on matching words in a search query with words in online resources, it is an inefficient method of finding information in a database. This matching fails to retrieve synonyms, and it also retrieves…

Literature searching for clinical and cost-effectiveness studies used in health technology assessment reports carried out for the National Institute for Clinical Excellence appraisal system.

PubMed

Royle, P; Waugh, N

2003-01-01

To contribute to making searching for Technology Assessment Reports (TARs) more cost-effective by suggesting an optimum literature retrieval strategy. A sample of 20 recent TARs. All sources used to search for clinical and cost-effectiveness studies were recorded. In addition, all studies that were included in the clinical and cost-effectiveness sections of the TARs were identified, and their characteristics recorded, including author, journal, year, study design, study size and quality score. Each was also classified by publication type, and then checked to see whether it was indexed in the following databases: MEDLINE, EMBASE, and then either the Cochrane Controlled Trials Register (CCTR) for clinical effectiveness studies or the NHS Economic Evaluation Database (NHS EED) for the cost-effectiveness studies. Any study not found in at least one of these databases was checked to see whether it was indexed in the Science Citation Index (SCI) and BIOSIS, and the American Society of Clinical Oncology (ASCO) Online if a cancer review. Any studies still not found were checked to see whether they were in a number of additional databases. The median number of sources searched per TAR was 20, and the range was from 13 to 33 sources. Six sources (CCTR, DARE, EMBASE, MEDLINE, NHS EED and sponsor/industry submissions to National Institute for Clinical Excellence) were used in all reviews. After searching the MEDLINE, EMBASE and NHS EED databases, 87.3% of the clinical effectiveness studies and 94.8% of the cost-effectiveness studies were found, rising to 98.2% when SCI, BIOSIS and ASCO Online and 97.9% when SCI and ASCO Online, respectively, were added. The median number of sources searched for the 14 TARs that included an economic model was 9.0 per TAR. A sensitive search filter for identifying non-randomised controlled trials (RCT), constructed for MEDLINE and using the search terms from the bibliographic records in the included studies, retrieved only 85% of the known sample. Therefore, it is recommended that when searching for non-RCT studies a search is done for the intervention alone, and records are then scanned manually for those that look relevant. Searching additional databases beyond the Cochrane Library (which includes CCTR, NHS EED and the HTA database), MEDLINE, EMBASE and SCI, plus BIOSIS limited to meeting abstracts only, was seldom found to be effective in retrieving additional studies for inclusion in the clinical and cost-effectiveness sections of TARs (apart from reviews of cancer therapies, where a search of the ASCO database is recommended). A more selective approach to database searching would suffice in most cases and would save resources, thereby making the TAR process more efficient. However, searching non-database sources (including submissions from manufacturers, recent meeting abstracts, contact with experts and checking reference lists) does appear to be a productive way of identifying further studies.

Metformin for Clozapine Associated Obesity: A Systematic Review and Meta-Analysis.

PubMed

Siskind, Dan J; Leung, Janni; Russell, Anthony W; Wysoczanski, Daniel; Kisely, Steve

2016-01-01

Although clozapine is the gold-standard for treatment refractory schizophrenia, it has the worst metabolic profile of all antipsychotics. This is partly mediated by clozapine's impact on glucagon-like peptide (GLP-1). There is an absence of robust evidence for effective treatments for clozapine associated weight gain and metabolic syndrome. Metformin, with its role in increasing GLP-1 may aid weight loss among people on clozapine. We conducted a systematic-review and meta-analysis of metformin versus placebo for change in weight and metabolic syndrome for people on clozapine without diabetes mellitus. We searched the Cochrane Schizophrenia Group's trial register, Pubmed and Embase, as well as the following Chinese databases: the Chinese Biomedical Literature Service System and China Knowledge Resource Integrated Database. This was supplemented by hand searches of key papers. Eight studies, of which three were from Chinese databases, with 478 participants were included. We found that metformin was superior to placebo in terms of weight loss (-3.12kg, 95%CI -4.88kg to -1.37kg) and BMI (-1.18kg/m2, 95%CI -1.76kg/m2 to -0.61kg/m2). Metformin significantly improved three of the five components of metabolic syndrome; waist circumference, fasting glucose and triglycerides. Sensitivity analysis on study quality and duration did not greatly impact results. Metformin led to clinically meaningful weight loss among people on clozapine, and may reduce the rates of metabolic syndrome. Inclusion of metformin into the treatment protocols of people on clozapine, as tolerated, should be considered. PROSPERO registration number: CRD42015029723.

Efficacy of cleaning products for C difficile

PubMed Central

MacLeod-Glover, Nora; Sadowski, Cheryl

2010-01-01

Abstract OBJECTIVE To review the evidence for the efficacy of products used for environmental or hand cleaning on the rates of Clostridium difficile–associated diarrhea (CDAD). QUALITY OF EVIDENCE MEDLINE, EMBASE, and the Cochrane Database of Systematic Reviews were searched for articles pertinent to the efficacy of cleaning products against C difficile or studies with outcomes related to rates of CDAD. Evidence was level II. MAIN MESSAGE Minimizing the incidence of CDAD in geriatric rehabilitation units is essential to achieving the goals of increasing patient function and independence for discharge into the community. Attention to environmental control of C difficile and its spores by health care workers and patient visitors is an important secondary prevention strategy. CONCLUSION Chlorine-releasing agents are more effective than detergents for killing spores produced by C difficile. No level I evidence is available to determine if the use of chlorine-releasing agents has an effect on rates of CDAD. Hand-washing is currently the recommended strategy for reducing transmission of C difficile. Alcohol gels do not inactivate C difficile spores; however, increased use of alcohol hand gel has not been associated with higher rates of CDAD. PMID:20463269

Efficacy of cleaning products for C. difficile: environmental strategies to reduce the spread of Clostridium difficile-associated diarrhea in geriatric rehabilitation.

PubMed

Macleod-Glover, Nora; Sadowski, Cheryl

2010-05-01

To review the evidence for the efficacy of products used for environmental or hand cleaning on the rates of Clostridium difficile-associated diarrhea (CDAD). MEDLINE, EMBASE, and the Cochrane Database of Systematic Reviews were searched for articles pertinent to the efficacy of cleaning products against C. difficile or studies with outcomes related to rates of CDAD. Evidence was level II. Minimizing the incidence of CDAD in geriatric rehabilitation units is essential to achieving the goals of increasing patient function and independence for discharge into the community. Attention to environmental control of C. difficile and its spores by health care workers and patient visitors is an important secondary prevention strategy. Chlorine-releasing agents are more effective than detergents for killing spores produced by C. difficile. No level I evidence is available to determine if the use of chlorine-releasing agents has an effect on rates of CDAD. Hand-washing is currently the recommended strategy for reducing transmission of C. difficile. Alcohol gels do not inactivate C. difficile spores; however, increased use of alcohol hand gel has not been associated with higher rates of CDAD.

Night Orthosis After Surgical Correction of Dupuytren Contractures: A Systematic Review.

PubMed

Samargandi, Osama A; Alyouha, Sarah; Larouche, Patricia; Corkum, Joseph P; Kemler, Marius A; Tang, David T

2017-10-01

To determine the role of night orthosis use after surgical correction of Dupuytren contracture. We searched MEDLINE, EMBASE, CINAHL, AMED, OTSeeker, and CENTRAL for articles published from inception of the databases to August 2015. Assessment was undertaken by 2 independent reviewers (O.A.S. and S.A.). Methodological quality of randomized controlled trials was assessed using the Cochrane risk of bias tool and the Newcastle-Ottawa instrument. Seven studies met the standard for inclusion in this review. A total of 659 patients across these 7 studies were included in the analysis, with follow-up ranging from 3 to 72 months. None of the included studies assessed recurrence. The analysis revealed no significant improvement in range of motion of hand joints for patients who received a static night orthosis after Dupuytren surgery compared with patients without an orthosis. Similarly, no differences were found in patient-reported functional status across the 2 groups. The current literature does not appear to support the use of static night orthosis in addition to hand therapy after surgical correction of Dupuytren contracture. Therapeutic IV. Copyright © 2017 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

Evidence-based librarianship: searching for the needed EBL evidence.

PubMed

Eldredge, J D

2000-01-01

This paper discusses the challenges of finding evidence needed to implement Evidence-Based Librarianship (EBL). Focusing first on database coverage for three health sciences librarianship journals, the article examines the information contents of different databases. Strategies are needed to search for relevant evidence in the library literature via these databases, and the problems associated with searching the grey literature of librarianship. Database coverage, plausible search strategies, and the grey literature of library science all pose challenges to finding the needed research evidence for practicing EBL. Health sciences librarians need to ensure that systems are designed that can track and provide access to needed research evidence to support Evidence-Based Librarianship (EBL).

MIDAS: a database-searching algorithm for metabolite identification in metabolomics.

PubMed

Wang, Yingfeng; Kora, Guruprasad; Bowen, Benjamin P; Pan, Chongle

2014-10-07

A database searching approach can be used for metabolite identification in metabolomics by matching measured tandem mass spectra (MS/MS) against the predicted fragments of metabolites in a database. Here, we present the open-source MIDAS algorithm (Metabolite Identification via Database Searching). To evaluate a metabolite-spectrum match (MSM), MIDAS first enumerates possible fragments from a metabolite by systematic bond dissociation, then calculates the plausibility of the fragments based on their fragmentation pathways, and finally scores the MSM to assess how well the experimental MS/MS spectrum from collision-induced dissociation (CID) is explained by the metabolite's predicted CID MS/MS spectrum. MIDAS was designed to search high-resolution tandem mass spectra acquired on time-of-flight or Orbitrap mass spectrometer against a metabolite database in an automated and high-throughput manner. The accuracy of metabolite identification by MIDAS was benchmarked using four sets of standard tandem mass spectra from MassBank. On average, for 77% of original spectra and 84% of composite spectra, MIDAS correctly ranked the true compounds as the first MSMs out of all MetaCyc metabolites as decoys. MIDAS correctly identified 46% more original spectra and 59% more composite spectra at the first MSMs than an existing database-searching algorithm, MetFrag. MIDAS was showcased by searching a published real-world measurement of a metabolome from Synechococcus sp. PCC 7002 against the MetaCyc metabolite database. MIDAS identified many metabolites missed in the previous study. MIDAS identifications should be considered only as candidate metabolites, which need to be confirmed using standard compounds. To facilitate manual validation, MIDAS provides annotated spectra for MSMs and labels observed mass spectral peaks with predicted fragments. The database searching and manual validation can be performed online at http://midas.omicsbio.org.

Use of Topical Corticosteroids in Dermatology: An Evidence-based Approach

PubMed Central

Das, Anupam; Panda, Saumya

2017-01-01

Topical corticosteroids (TCs) are the pillars of dermatotherapeutics. These drugs are the “magic molecules,” provided they are used judiciously and appropriately, following a rational prescription. On exhaustive literature search in multiple databases, we found a significant evidence favoring the use of TCs in atopic eczema, localized vitiligo, psoriasis, chronic hand eczema, and localized bullous pemphigoid. However, contrary to conventional wisdom, we did not find any high-level scientific evidence in support of prescribing TCs in cutaneous lichen planus, sarcoidosis, and seborrhoeic dermatitis. Besides, evidence clearly advocates judicious use of mild-to-moderate corticosteroids (if required) in pregnancy and lactation and there is no risk of any fetal abnormality. PMID:28584365

Systematic literature review of incidence rates of low-speed vehicle run-over incidents in children.

PubMed

Griffin, Bronwyn; Watt, Kerrieanne; Kimble, Roy; Wallis, Belinda; Shields, Linda

2014-04-01

To systematically review the literature investigating the incidence of fatal and or nonfatal low-speed vehicle run-over (LSVRO) incidents in children aged 0-15 years. The following databases were searched using specific search terms, from their date of conception up to June 2011: Cochrane Library, Medline, CINAHL, Embase, AMI, Sociological Abstracts, ERIC, PsycArticles, PsycInfo, Urban Studies and Planning; Australian Criminology Database; Dissertations and Thesis; Academic Research Library; Social Services Abstracts; Family and Society; Scopus; and Web of Science. A total of 128 articles were identified in the databases (33 found by hand searching). The title and abstract of these were read, and 102 were removed because they were not primary research articles relating to LSVRO-type injuries. Twenty-six articles were assessed against the inclusion (reporting population level incidence rates) and exclusion criteria, 19 of which were excluded, leaving a total of five articles for inclusion in the review. Five studies were identified that met the inclusion criteria. The incidence rate in nonfatal LSVRO events varied in the range of 7.09 to 14.79 per 100,000 and from 0.63 to 3.2 per 100,000 in fatal events. Using International Classification of Diseases codes for classifying fatal or nonfatal LSVRO incidents is problematic as there is no specific code for LSVRO. The current body of research is void of a comprehensive secular population data analysis. Only with an improved spectrum of incidence rates will appropriate evaluation of this problem be possible, and this will inform nursing prevention interventions. The effect of LSVRO incidents is clearly understudied. More research is required to address incidence rates in relation to culture, environment, risk factors, car design, and injury characteristics. The lack of nursing research or policy around this area of injury, most often to children, indicates a field of inquiry and policy development that needs attention. © 2013 Sigma Theta Tau International.

Worldwide pattern of antibiotic prescription in endodontic infections.

PubMed

Segura-Egea, Juan José; Martín-González, Jenifer; Jiménez-Sánchez, María Del Carmen; Crespo-Gallardo, Isabel; Saúco-Márquez, Juan José; Velasco-Ortega, Eugenio

2017-08-01

Odontogenic infections, and especially endodontic infections, are polymicrobial, involving a combination of Gram-positive and Gram-negative facultative anaerobes and strictly anaerobic bacteria. Therefore, antibiotics can be used as an adjunct to endodontic treatment. However, most chronic and even acute endodontic infections can be successfully managed by disinfection of the root-canal system, which eliminates the source of infection, followed by abscess drainage or tooth extraction, without the need for antibiotics. The literature provides evidence of inadequate prescribing practices by dentists. The aim of this concise review was to analyse the worldwide pattern of antibiotic prescription in endodontic infections. Comprehensive searches were conducted in MEDLINE/PubMed, Wiley Online Database, Web of Science and Scopus. The databases were searched up to 13 March 2016 for studies in which dentists used systemic antibiotics to treat endodontic lesions and which reported data on the type of antibiotic prescribed and on the diagnosis of the endodontic disease treated. The electronic and hand searches identified 69 titles, of which 25 were included in the final analysis. Amoxicillin was reported as the drug of choice for endodontic infections in most countries, and clindamycin and erythromycin were the choice for patients allergic to penicillin. Dentists worldwide prescribe antibiotics for non-indicated conditions, such as pulpitis. Antibiotics are overprescribed for the management of endodontic infections. It is necessary to improve antibiotic-prescribing habits in the treatment of endodontic infections, as well as to introduce educational initiatives to encourage the coherent and proper use of antibiotics in such conditions. © 2017 FDI World Dental Federation.

Therapeutic Alliances in Stroke Rehabilitation: A Meta-Ethnography.

PubMed

Lawton, Michelle; Haddock, Gillian; Conroy, Paul; Sage, Karen

2016-11-01

To synthesize qualitative studies exploring patients' and professionals' perspectives and experiences of developing and maintaining therapeutic alliances in stroke rehabilitation. A systematic literature search was conducted using the following electronic databases: PsycINFO, CINAHL, Embase, MEDLINE, Allied and Complementary Medicine Database, Applied Social Sciences Index and Abstracts, and ComDisDome from inception to May 2014. This was supplemented by hand searching, reference tracking, generic web searching, and e-mail contact with experts. Qualitative peer reviewed articles reporting experiences or perceptions of the patient or professional in relation to therapeutic alliance construction and maintenance in stroke rehabilitation were selected for inclusion. After a process of exclusion, 17 publications were included in the synthesis. All text identified in the results and discussion sections of the selected studies were extracted verbatim for analysis in a qualitative software program. Studies were critically appraised independently by 2 reviewers. Articles were synthesized using a technique of meta-ethnography. Four overarching themes emerged from the process of reciprocal translation: (1) the professional-patient relationship: degree of connectedness; (2) asymmetrical contributions; (3) the process of collaboration: finding the middle ground; and (4) system drivers. The findings from the meta-ethnography suggest that the balance of power between the patient and professional is asymmetrically distributed in the construction of the alliance. However, given that none of the studies included in the review addressed therapeutic alliance as a primary research area, further research is required to develop a conceptual framework relevant to stroke rehabilitation, in order to determine how this construct contributes to treatment efficacy. Copyright © 2016 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Advantages and Challenges of Dried Blood Spot Analysis by Mass Spectrometry Across the Total Testing Process.

PubMed

Zakaria, Rosita; Allen, Katrina J; Koplin, Jennifer J; Roche, Peter; Greaves, Ronda F

2016-12-01

Through the introduction of advanced analytical techniques and improved throughput, the scope of dried blood spot testing utilising mass spectrometric methods, has broadly expanded. Clinicians and researchers have become very enthusiastic about the potential applications of dried blood spot based mass spectrometric applications. Analysts on the other hand face challenges of sensitivity, reproducibility and overall accuracy of dried blood spot quantification. In this review, we aim to bring together these two facets to discuss the advantages and current challenges of non-newborn screening applications of dried blood spot quantification by mass spectrometry. To address these aims we performed a key word search of the PubMed and MEDLINE online databases in conjunction with individual manual searches to gather information. Keywords for the initial search included; "blood spot" and "mass spectrometry"; while excluding "newborn"; and "neonate". In addition, databases were restricted to English language and human specific. There was no time period limit applied. As a result of these selection criteria, 194 references were identified for review. For presentation, this information is divided into: 1) clinical applications; and 2) analytical considerations across the total testing process; being pre-analytical, analytical and post-analytical considerations. DBS analysis using MS applications is now broadly applied, with drug monitoring for both therapeutic and toxicological analysis being the most extensively reported. Several parameters can affect the accuracy of DBS measurement and further bridge experiments are required to develop adjustment rules for comparability between dried blood spot measures and the equivalent serum/plasma values. Likewise, the establishment of independent reference intervals for dried blood spot sample matrix is required.

System, method and apparatus for conducting a keyterm search

NASA Technical Reports Server (NTRS)

McGreevy, Michael W. (Inventor)

2004-01-01

A keyterm search is a method of searching a database for subsets of the database that are relevant to an input query. First, a number of relational models of subsets of a database are provided. A query is then input. The query can include one or more keyterms. Next, a gleaning model of the query is created. The gleaning model of the query is then compared to each one of the relational models of subsets of the database. The identifiers of the relevant subsets are then output.

System, method and apparatus for conducting a phrase search

NASA Technical Reports Server (NTRS)

McGreevy, Michael W. (Inventor)

2004-01-01

A phrase search is a method of searching a database for subsets of the database that are relevant to an input query. First, a number of relational models of subsets of a database are provided. A query is then input. The query can include one or more sequences of terms. Next, a relational model of the query is created. The relational model of the query is then compared to each one of the relational models of subsets of the database. The identifiers of the relevant subsets are then output.

On Building a Search Interface Discovery System

NASA Astrophysics Data System (ADS)

Shestakov, Denis

A huge portion of the Web known as the deep Web is accessible via search interfaces to myriads of databases on the Web. While relatively good approaches for querying the contents of web databases have been recently proposed, one cannot fully utilize them having most search interfaces unlocated. Thus, the automatic recognition of search interfaces to online databases is crucial for any application accessing the deep Web. This paper describes the architecture of the I-Crawler, a system for finding and classifying search interfaces. The I-Crawler is intentionally designed to be used in the deep web characterization surveys and for constructing directories of deep web resources.

Discrete Event Simulation-Based Resource Modelling in Health Technology Assessment.

PubMed

Salleh, Syed; Thokala, Praveen; Brennan, Alan; Hughes, Ruby; Dixon, Simon

2017-10-01

The objective of this article was to conduct a systematic review of published research on the use of discrete event simulation (DES) for resource modelling (RM) in health technology assessment (HTA). RM is broadly defined as incorporating and measuring effects of constraints on physical resources (e.g. beds, doctors, nurses) in HTA models. Systematic literature searches were conducted in academic databases (JSTOR, SAGE, SPRINGER, SCOPUS, IEEE, Science Direct, PubMed, EMBASE) and grey literature (Google Scholar, NHS journal library), enhanced by manual searchers (i.e. reference list checking, citation searching and hand-searching techniques). The search strategy yielded 4117 potentially relevant citations. Following the screening and manual searches, ten articles were included. Reviewing these articles provided insights into the applications of RM: firstly, different types of economic analyses, model settings, RM and cost-effectiveness analysis (CEA) outcomes were identified. Secondly, variation in the characteristics of the constraints such as types and nature of constraints and sources of data for the constraints were identified. Thirdly, it was found that including the effects of constraints caused the CEA results to change in these articles. The review found that DES proved to be an effective technique for RM but there were only a small number of studies applied in HTA. However, these studies showed the important consequences of modelling physical constraints and point to the need for a framework to be developed to guide future applications of this approach.

Healthcare needs of older Arab migrants: a systematic review.

PubMed

Al Abed, Naser A; Davidson, Patricia M; Hickman, Louise D

2014-07-01

To explore the healthcare needs of older Arab migrants, focussing on Arab-Australians and their socio-cultural characteristics. Disparities in accessing healthcare services and addressing healthcare needs are evident among ethnic minorities including Arab migrants, particularly, older people. Racial stereotyping can also affect their ability to use these services. Arabs are a populous and diverse group with a long history of global migration. Australia is one of the most multicultural societies in the world, and Arab-Australians constitute an important ethnic minority group. Systematic review. The electronic databases Academic Search Complete (EBSCO), MEDLINE (Ovid), Ageline, ProQuest, CINAHL, PubMed, PsychINFO and Google Scholar were searched from 1990-October 2012. Search terms included health care needs, aged care, ethnic, cultural, linguistics, social, ethnic groups, culturally and linguistically diverse, nonEnglish speaking, ageing, elderly, Arabs, Arabic-speaking and Australia. Eight articles reviewing the healthcare issues of Australians from Arabic-speaking background were identified using the search strategy. An additional eight articles were identified through hand searching. Racial stereotyping can alter health-seeking behaviours and healthcare treatment. Increasing the understanding of specific cultural attributes of Arab-Australians will contribute to improving health outcomes. Healthcare providers and policymakers need to adopt more effective ways of communication with Arab-Australians to provide more culturally competent care and achieve better health outcomes. © 2013 John Wiley & Sons Ltd.

The disconnect between evidence and practice: a systematic review of person-centred interventions and training manuals for care home staff working with people with dementia.

PubMed

Fossey, Jane; Masson, Sarah; Stafford, Jane; Lawrence, Vanessa; Corbett, Anne; Ballard, Clive

2014-08-01

The overall objective is to determine the availability of person-centred intervention and training manuals for dementia care staff with clinical trial evidence of efficacy. Interventions were identified using a search of electronic databases, augmented by mainstream search engines, reference lists, hand searching for resources and consultation with an expert panel. The specific search for published manuals was complemented by a search for randomised control trials focussing on training and activity-based interventions for people with dementia in care homes. Manuals were screened for eligibility and rated to assess their quality, relevance and feasibility. A meta-analysis of randomised control trials indicated that person-centred training interventions conferred significant benefit in improving agitation and reducing the use of antipsychotics. Each of the efficacious packages included a sustained period of joint working and supervision with a trained mental health professional in addition to an educational element. However, of the 170 manuals that were identified, 30 met the quality criteria and only four had been evaluated in clinical trials. Despite the availability of a small number of evidence-based training manuals, there is a widespread use of person-centred intervention and training manuals that are not evidence-based. Clearer guidance is needed to ensure that commissioned training and interventions are based on robust evidence. Copyright © 2014 John Wiley & Sons, Ltd.

A review on quantum search algorithms

NASA Astrophysics Data System (ADS)

Giri, Pulak Ranjan; Korepin, Vladimir E.

2017-12-01

The use of superposition of states in quantum computation, known as quantum parallelism, has significant advantage in terms of speed over the classical computation. It is evident from the early invented quantum algorithms such as Deutsch's algorithm, Deutsch-Jozsa algorithm and its variation as Bernstein-Vazirani algorithm, Simon algorithm, Shor's algorithms, etc. Quantum parallelism also significantly speeds up the database search algorithm, which is important in computer science because it comes as a subroutine in many important algorithms. Quantum database search of Grover achieves the task of finding the target element in an unsorted database in a time quadratically faster than the classical computer. We review Grover's quantum search algorithms for a singe and multiple target elements in a database. The partial search algorithm of Grover and Radhakrishnan and its optimization by Korepin called GRK algorithm are also discussed.

Theories of behaviour and behaviour change across the social and behavioural sciences: a scoping review.

PubMed

Davis, Rachel; Campbell, Rona; Hildon, Zoe; Hobbs, Lorna; Michie, Susan

2015-01-01

Interventions to change health-related behaviours typically have modest effects and may be more effective if grounded in appropriate theory. Most theories applied to public health interventions tend to emphasise individual capabilities and motivation, with limited reference to context and social factors. Intervention effectiveness may be increased by drawing on a wider range of theories incorporating social, cultural and economic factors that influence behaviour. The primary aim of this paper is to identify theories of behaviour and behaviour change of potential relevance to public health interventions across four scientific disciplines: psychology, sociology, anthropology and economics. We report in detail the methodology of our scoping review used to identify these theories including which involved a systematic search of electronic databases, consultation with a multidisciplinary advisory group, web searching, searching of reference lists and hand searching of key behavioural science journals. Of secondary interest we developed a list of agreed criteria for judging the quality of the theories. We identified 82 theories and 9 criteria for assessing theory quality. The potential relevance of this wide-ranging number of theories to public health interventions and the ease and usefulness of evaluating the theories in terms of the quality criteria are however yet to be determined.

Bilingual and Home Language Interventions With Young Dual Language Learners: A Research Synthesis.

PubMed

Durán, Lillian K; Hartzheim, Daphne; Lund, Emily M; Simonsmeier, Vicki; Kohlmeier, Theresa L

2016-10-01

The purpose of this systematic review was to determine what bilingual or home language interventions have been found to be effective for 2- to 6-year-old dual language learners who have language impairment (LI) or are at risk for LI. We conducted ancestral searches and searches of electronic databases, hand-searched article bibliographies, and searched 19 journals for experimental, quasiexperimental, or single-subject studies. The review yielded 26 studies that were coded for quality, frequency and duration of the intervention, number of participants, location of intervention, interventionist, language(s) of intervention, and reported or calculated effect sizes. Studies were grouped by those that focused specifically on at-risk populations and those that focused on children with LI. Emerging trends provide support for bilingual and/or home language interventions for both children with LI and those at risk for LI. There were relatively few studies that met inclusion criteria, and the average quality rating for a study was 6.8 out of 9.0 possible points. More high-quality research is needed, particularly with populations that speak languages other than Spanish. Clinicians need more evidence-based recommendations to improve the language and literacy outcomes of the diverse range of dual language learners served in the United States and abroad.

Theories of behaviour and behaviour change across the social and behavioural sciences: a scoping review

PubMed Central

Davis, Rachel; Campbell, Rona; Hildon, Zoe; Hobbs, Lorna; Michie, Susan

2015-01-01

Interventions to change health-related behaviours typically have modest effects and may be more effective if grounded in appropriate theory. Most theories applied to public health interventions tend to emphasise individual capabilities and motivation, with limited reference to context and social factors. Intervention effectiveness may be increased by drawing on a wider range of theories incorporating social, cultural and economic factors that influence behaviour. The primary aim of this paper is to identify theories of behaviour and behaviour change of potential relevance to public health interventions across four scientific disciplines: psychology, sociology, anthropology and economics. We report in detail the methodology of our scoping review used to identify these theories including which involved a systematic search of electronic databases, consultation with a multidisciplinary advisory group, web searching, searching of reference lists and hand searching of key behavioural science journals. Of secondary interest we developed a list of agreed criteria for judging the quality of the theories. We identified 82 theories and 9 criteria for assessing theory quality. The potential relevance of this wide-ranging number of theories to public health interventions and the ease and usefulness of evaluating the theories in terms of the quality criteria are however yet to be determined. PMID:25104107

Mathematical Notation in Bibliographic Databases.

ERIC Educational Resources Information Center

Pasterczyk, Catherine E.

1990-01-01

Discusses ways in which using mathematical symbols to search online bibliographic databases in scientific and technical areas can improve search results. The representations used for Greek letters, relations, binary operators, arrows, and miscellaneous special symbols in the MathSci, Inspec, Compendex, and Chemical Abstracts databases are…

The Boolean Is Dead, Long Live the Boolean! Natural Language versus Boolean Searching in Introductory Undergraduate Instruction

ERIC Educational Resources Information Center

Lowe, M. Sara; Maxson, Bronwen K.; Stone, Sean M.; Miller, Willie; Snajdr, Eric; Hanna, Kathleen

2018-01-01

Boolean logic can be a difficult concept for first-year, introductory students to grasp. This paper compares the results of Boolean and natural language searching across several databases with searches created from student research questions. Performance differences between databases varied. Overall, natural search language is at least as good as…

Influence of muscle strength on early mobility in critically ill adult patients: Systematic literature review.

PubMed

Roberson, Audrey R; Starkweather, Angela; Grossman, Catherine; Acevedo, Edmund; Salyer, Jeanne

Muscle strength may be one indicator of readiness to mobilize that can be used to guide decisions regarding early mobility efforts and to progressively advance mobilization. To provide a synthesis of current measures of muscle strength in the assessment of early mobilization in critically ill adult patients who are receiving MV therapy. Research studies conducted between 2000-2015 were identified using PubMed, CINHAL, MEDLINE, and the Cochrane Database of Systematic Reviews databases using the search terms "muscle strength", "intensive care", "mechanical ventilation" and "muscle weakness". Nine articles used manual muscle testing, the Medical Research Council scale and/or hand-held dynamometer to provide objective measures for assessing muscle strength in the critically ill adult patient population. Further research is needed to examine the application of standardized measures of muscle strength for guiding decisions regarding early and progressive advancement of mobility goals in adult ICU patients on MV. Copyright © 2017 Elsevier Inc. All rights reserved.

Direct, indirect and intangible costs of acute hand and wrist injuries: A systematic review.

PubMed

Robinson, Luke Steven; Sarkies, Mitchell; Brown, Ted; O'Brien, Lisa

2016-12-01

Injuries sustained to the hand and wrist are common, accounting for 20% of all emergency presentations. The economic burden of these injuries, comprised of direct (medical expenses incurred), indirect (value of lost productivity) and intangible costs, can be extensive and rise sharply with the increase of severity. This paper systematically reviews cost-of-illness studies and health economic evaluations of acute hand and wrist injuries with a particular focus on direct, indirect and intangible costs. It aims to provide economic cost estimates of burden and discuss the cost components used in international literature. A search of cost-of-illness studies and health economic evaluations of acute hand and wrist injuries in various databases was conducted. Data extracted for each included study were: design, population, intervention, and estimates and measurement methodologies of direct, indirect and intangible costs. Reported costs were converted into US-dollars using historical exchange rates and then adjusted into 2015 US-dollars using an inflation calculator RESULTS: The search yielded 764 studies, of which 21 met the inclusion criteria. Twelve studies were cost-of-illness studies, and seven were health economic evaluations. The methodology used to derive direct, indirect and intangible costs differed markedly across all studies. Indirect costs represented a large portion of total cost in both cost-of-illness studies [64.5% (IQR 50.75-88.25)] and health economic evaluations [68% (IQR 49.25-73.5)]. The median total cost per case of all injury types was US$6951 (IQR $3357-$22,274) for cost-of-illness studies and US$8297 (IQR $3858-$33,939) for health economic evaluations. Few studies reported intangible cost data associated with acute hand and wrist injuries. Several studies have attempted to estimate the direct, indirect and intangible costs associated with acute hand and wrist injuries in various countries using heterogeneous methodologies. Estimates of the economic costs of different acute hand and wrist injuries varied greatly depending on the study methodology, however, by any standards, these injuries should be considered a substantial burden on the individual and society. Further research using standardised methodologies could provide guidance to relevant policy makers on how to best distribute limited resources by identifying the major disorders and exposures resulting in the largest burden. Copyright © 2016 Elsevier Ltd. All rights reserved.

A World Wide Web (WWW) server database engine for an organelle database, MitoDat.

PubMed

Lemkin, P F; Chipperfield, M; Merril, C; Zullo, S

1996-03-01

We describe a simple database search engine "dbEngine" which may be used to quickly create a searchable database on a World Wide Web (WWW) server. Data may be prepared from spreadsheet programs (such as Excel, etc.) or from tables exported from relationship database systems. This Common Gateway Interface (CGI-BIN) program is used with a WWW server such as available commercially, or from National Center for Supercomputer Algorithms (NCSA) or CERN. Its capabilities include: (i) searching records by combinations of terms connected with ANDs or ORs; (ii) returning search results as hypertext links to other WWW database servers; (iii) mapping lists of literature reference identifiers to the full references; (iv) creating bidirectional hypertext links between pictures and the database. DbEngine has been used to support the MitoDat database (Mendelian and non-Mendelian inheritance associated with the Mitochondrion) on the WWW.

A comprehensive and scalable database search system for metaproteomics.

PubMed

Chatterjee, Sandip; Stupp, Gregory S; Park, Sung Kyu Robin; Ducom, Jean-Christophe; Yates, John R; Su, Andrew I; Wolan, Dennis W

2016-08-16

Mass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size of their sequence databases, which severely restricts the proteomic sequencing depth and functional analysis of highly complex samples. The growing amount of public high-throughput sequencing data will only exacerbate this problem. We designed a broadly applicable metaproteomic analysis method (ComPIL) that addresses protein database size limitations. Our approach to overcome this significant limitation in metaproteomics was to design a scalable set of sequence databases assembled for optimal library querying speeds. ComPIL was integrated with a modified version of the search engine ProLuCID (termed "Blazmass") to permit rapid matching of experimental spectra. Proof-of-principle analysis of human HEK293 lysate with a ComPIL database derived from high-quality genomic libraries was able to detect nearly all of the same peptides as a search with a human database (~500x fewer peptides in the database), with a small reduction in sensitivity. We were also able to detect proteins from the adenovirus used to immortalize these cells. We applied our method to a set of healthy human gut microbiome proteomic samples and showed a substantial increase in the number of identified peptides and proteins compared to previous metaproteomic analyses, while retaining a high degree of protein identification accuracy and allowing for a more in-depth characterization of the functional landscape of the samples. The combination of ComPIL with Blazmass allows proteomic searches to be performed with database sizes much larger than previously possible. These large database searches can be applied to complex meta-samples with unknown composition or proteomic samples where unexpected proteins may be identified. The protein database, proteomic search engine, and the proteomic data files for the 5 microbiome samples characterized and discussed herein are open source and available for use and additional analysis.

Network meta-analyses could be improved by searching more sources and by involving a librarian.

PubMed

Li, Lun; Tian, Jinhui; Tian, Hongliang; Moher, David; Liang, Fuxiang; Jiang, Tongxiao; Yao, Liang; Yang, Kehu

2014-09-01

Network meta-analyses (NMAs) aim to rank the benefits (or harms) of interventions, based on all available randomized controlled trials. Thus, the identification of relevant data is critical. We assessed the conduct of the literature searches in NMAs. Published NMAs were retrieved by searching electronic bibliographic databases and other sources. Two independent reviewers selected studies and five trained reviewers abstracted data regarding literature searches, in duplicate. Search method details were examined using descriptive statistics. Two hundred forty-nine NMAs were included. Eight used previous systematic reviews to identify primary studies without further searching, and five did not report any literature searches. In the 236 studies that used electronic databases to identify primary studies, the median number of databases was 3 (interquartile range: 3-5). MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials were the most commonly used databases. The most common supplemental search methods included reference lists of included studies (48%), reference lists of previous systematic reviews (40%), and clinical trial registries (32%). None of these supplemental methods was conducted in more than 50% of the NMAs. Literature searches in NMAs could be improved by searching more sources, and by involving a librarian or information specialist. Copyright © 2014 Elsevier Inc. All rights reserved.

Development of a Dependency Theory Toolbox for Database Design.

DTIC Science & Technology

1987-12-01

published algorithms and theorems , and hand simulating these algorithms can be a tedious and error prone chore. Additionally, since the process of...to design and study relational databases exists in the form of published algorithms and theorems . However, hand simulating these algorithms can be a...published algorithms and theorems . Hand simulating these algorithms can be a tedious and error prone chore. Therefore, a toolbox of algorithms and

Hierarchy of evidence relating to hand surgery in Brazilian orthopedic journals.

PubMed

Moraes, Vinícius Ynoe de; Belloti, João Carlos; Moraes, Fábio Ynoe de; Galbiatti, José Antonio; Palácio, Evandro Pereira; Santos, João Baptista Gomes Dos; Faloppa, Flávio

2011-03-01

There is no systematic assessment of the quality of scientific production in the specialty of hand surgery in our setting. This study aimed to systematically assess the status of evidence generation relating to hand surgery and to evaluate the reproducibility of the classification method based on an evidence pyramid. Secondary study conducted at Universidade Federal de São Paulo (Unifesp) and Faculdade Estadual de Medicina de Marília (Famema). Two researchers independently conducted an electronic database search for hand surgery studies published between 2000 and 2009 in the two main Brazilian orthopedic journals (Acta Ortopédica Brasileira and Revista Brasileira de Ortopedia). The studies identified were subsequently classified according to methodological design (systematic review of the literature, randomized clinical trial, cohort study, case-control study, case series and other studies) and evidence level (I to V). A total of 1,150 articles were evaluated, and 83 (7.2%) were included in the final analysis. Studies with evidence level IV (case series) accounted for 41 (49%) of the published papers. Studies with evidence level V (other studies) accounted for 12 (14.5%) of the papers. Only two studies (2.4%) were ranked as level I or II. The inter-rater reproducibility was excellent (k = 0.94). Hand surgery articles corresponded to less than one tenth of Brazilian orthopedic production. Studies with evidence level IV were the commonest type. The reproducibility of the classification stratified by evidence level was almost perfect.

Fragrance allergy in patients with hand eczema - a clinical study.

PubMed

Heydorn, Siri; Johansen, Jeanne Duus; Andersen, Klaus E; Bruze, Magnus; Svedman, Cecilia; White, Ian R; Basketter, David A; Menné, Torkil

2003-06-01

Fragrance allergy and hand eczema are both common among dermatological patients. Fragrance mix (FM) and its constituents have a recognized relevance to exposure to fine fragrances and cosmetic products. Based on extensive chemical analysis and database search, a new selection of fragrances was established, including 14 known fragrance allergens present in products to which hand exposure would occur. A non-irritating patch-test concentration for some fragrances was established in 212 consecutive patients. 658 consecutive patients presenting with hand eczema were patch tested with the European standard series and the developed selection of fragrances. 67 (10.2%) of the 658 patients had a positive reaction to 1 or more of our selection of fragrance chemicals present in the new selection. The most common reactions to fragrances not included in the FM were to citral, Lyral (hydroxyisohexyl-3-cyclohexene carboxaldehyde) and oxidized l-limonene. A concomitant reaction to the FM identified potential fragrance allergy in less than (1/2) of these patients. Exposure assessment and a statistically significant association between a positive patch test to our selected fragrances and patients' history support the relevance of this selection of fragrances. Those with a positive reaction to our selected fragrances were significantly more likely to have 1 or more positive patch tests in the standard series. This observation is the basis for the hypothesis concerning cross-reactivity and the effect of simultaneous exposure. The study found that fragrance allergy could be a common problem in patients with eczema on the hands.

Teaching Data Base Search Strategies.

ERIC Educational Resources Information Center

Hannah, Larry

1987-01-01

Discusses database searching as a method for developing thinking skills, and describes an activity suitable for fifth grade through high school using a president's and vice president's database. Teaching methods are presented, including student team activities, and worksheets designed for the AppleWorks database are included. (LRW)

A Web-based Tool for SDSS and 2MASS Database Searches

NASA Astrophysics Data System (ADS)

Hendrickson, M. A.; Uomoto, A.; Golimowski, D. A.

We have developed a web site using HTML, Php, Python, and MySQL that extracts, processes, and displays data from the Sloan Digital Sky Survey (SDSS) and the Two-Micron All-Sky Survey (2MASS). The goal is to locate brown dwarf candidates in the SDSS database by looking at color cuts; however, this site could also be useful for targeted searches of other databases as well. MySQL databases are created from broad searches of SDSS and 2MASS data. Broad queries on the SDSS and 2MASS database servers are run weekly so that observers have the most up-to-date information from which to select candidates for observation. Observers can look at detailed information about specific objects including finding charts, images, and available spectra. In addition, updates from previous observations can be added by any collaborators; this format makes observational collaboration simple. Observers can also restrict the database search, just before or during an observing run, to select objects of special interest.

Ophthalmology and vision science research: part 5: surfing or sieving--using literature databases wisely.

PubMed

Sherwin, Trevor; Gilhotra, Amardeep K

2006-02-01

Literature databases are an ever-expanding resource available to the field of medical sciences. Understanding how to use such databases efficiently is critical for those involved in research. However, for the uninitiated, getting started is a major hurdle to overcome and for the occasional user, the finer points of database searching remain an unacquired skill. In the fifth and final article in this series aimed at those embarking on ophthalmology and vision science research, we look at how the beginning researcher can start to use literature databases and, by using a stepwise approach, how they can optimize their use. This instructional paper gives a hypothetical example of a researcher writing a review article and how he or she acquires the necessary scientific literature for the article. A prototype search of the Medline database is used to illustrate how even a novice might swiftly acquire the skills required for a medium-level search. It provides examples and key tips that can increase the proficiency of the occasional user. Pitfalls of database searching are discussed, as are the limitations of which the user should be aware.

Critical factors for the success of orthodontic mini-implants: a systematic review.

PubMed

Chen, Yan; Kyung, Hee Moon; Zhao, Wen Ting; Yu, Won Jae

2009-03-01

This systematic review was undertaken to discuss factors that affect mini-implants as direct and indirect orthodontic anchorage. The data were collected from electronic databases (Medline [Entrez PubMed], Embase, Web of Science, Cochrane Library, and All Evidence Based Medicine Reviews). Randomized clinical trials, prospective and retrospective clinical studies, and clinical trials concerning the properties, affective factors, and requirements of mini-implants were considered. The titles and abstracts that appeared to fulfill the initial selection criteria were collected by consensus, and the original articles were retrieved and evaluated with a methodologic checklist. A hand search of key orthodontic journals was performed to identify recent unindexed literature. The search strategy resulted in 596 articles. By screening titles and abstracts, 126 articles were identified. After the exclusion criteria were applied, 16 articles remained. The analyzed results of the literature were divided into 2 topics: placement-related and loading-related factors. Mini-implants are effective as anchorage, and their success depends on proper initial mechanical stability and loading quality and quantity.

The impact of nurse prescribing on the clinical setting.

PubMed

Creedon, Rena; Byrne, Stephen; Kennedy, Julia; McCarthy, Suzanne

To investigate the impact nurse prescribing has on the organisation, patient and health professional, and to identify factors associated with the growth of nurse prescribing. Systematic search and narrative review. Data obtained through CINAHL, PubMed, Science direct, Online Computer Library Centre (OCLC), databases/websites, and hand searching. English peer-reviewed quantitative, qualitative and mixed-method articles published from September 2009 through to August 2014 exploring nurse prescribing from the perspective of the organisation, health professional and patient were included. Following a systematic selection process, studies identified were also assessed for quality by applying Cardwell's framework. From the initial 443 citations 37 studies were included in the review. Most studies were descriptive in nature. Commonalities addressed were stakeholders' views, prescribing in practice, jurisdiction, education and benefits/barriers. Prescriptive authority for nurses continues to be a positive addition to clinical practice. However, concerns have emerged regarding appropriate support, relationships and jurisdictional issues. A more comprehensive understanding of nurse and midwife prescribing workloads is required to capture the true impact and cost-effectiveness of the initiative.

Role stress in nurses: review of related factors and strategies for moving forward.

PubMed

Chang, Esther M; Hancock, Karen M; Johnson, Amanda; Daly, John; Jackson, Debra

2005-03-01

The aim of this paper was to review the literature on factors related to role stress in nurses, and present strategies for addressing this issue based on the findings of this review while considering potential areas for development and research. Computerized databases were searched as well as hand searching of articles in order to conduct this review. This review identified multiple factors related to the experience of role stress in nurses. Role stress, in particular, work overload, has been reported as one of the main reasons for nurses leaving the workforce. This paper concludes that it is a priority to find new and innovative ways of supporting nurses in their experience of role stress. Some examples discussed in this article include use of stress education and management strategies; team-building strategies; balancing priorities; enhancing social and peer support; flexibility in work hours; protocols to deal with violence; and retention and attraction of nursing staff strategies. These strategies need to be empirically evaluated for their efficacy in reducing role stress.

Topical capsaicin for pain in osteoarthritis: A literature review.

PubMed

Guedes, Vânia; Castro, João Paulo; Brito, Iva

Osteoarthritis is the most common joint disorder worldwide. The predominant symptom, pain, is usually treated with acetaminophen or oral non-steroidal anti-inflammatory drugs, although they are associated with a significant risk of side effects. Topical capsaicin may represent an effective and safe alternative. The aim of this review is to examine the evidence for the efficacy and safety profile of topical capsaicin in the management of pain caused by osteoarthritis. Databases were searched for articles published between 2004 and 2016, in Portuguese, English or Spanish, using the search terms "capsaicin" and "osteoarthritis". When compared to placebo, it was found that topical capsaicin has a good safety profile and efficacy in reducing osteoarthritis pain of the hand, knee, hip or shoulder. However, the studies have significant limitations, the most important the difficulty of blinding. It is attributed to this review the strength of recommendation B. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Reumatología y Colegio Mexicano de Reumatología. All rights reserved.

Part-based deep representation for product tagging and search

NASA Astrophysics Data System (ADS)

Chen, Keqing

2017-06-01

Despite previous studies, tagging and indexing the product images remain challenging due to the large inner-class variation of the products. In the traditional methods, the quantized hand-crafted features such as SIFTs are extracted as the representation of the product images, which are not discriminative enough to handle the inner-class variation. For discriminative image representation, this paper firstly presents a novel deep convolutional neural networks (DCNNs) architect true pre-trained on a large-scale general image dataset. Compared to the traditional features, our DCNNs representation is of more discriminative power with fewer dimensions. Moreover, we incorporate the part-based model into the framework to overcome the negative effect of bad alignment and cluttered background and hence the descriptive ability of the deep representation is further enhanced. Finally, we collect and contribute a well-labeled shoe image database, i.e., the TBShoes, on which we apply the part-based deep representation for product image tagging and search, respectively. The experimental results highlight the advantages of the proposed part-based deep representation.

The Efficacy of Auditory Perceptual Training for Tinnitus: A Systematic Review

PubMed Central

Stacey, Paula C.; Hall, Deborah A.

2010-01-01

Auditory perceptual training affects neural plasticity and so represents a potential strategy for tinnitus management. We assessed the effects of auditory perceptual training on tinnitus perception and/or its intrusiveness via a systematic review of published literature. An electronic database search using the keywords ‘tinnitus and learning’ or ‘tinnitus and training’ was conducted, updated by a hand search. The ten studies identified were reviewed independently by two reviewers, data were extracted, study quality was assessed according to a number of specific criteria and the information was synthesised using a narrative approach. Nine out of the ten studies reported some significant change in either self-reported or psychoacoustic outcome measures after auditory training. However, all studies were quality rated as providing low or moderate levels of evidence for an effect. We identify a need for appropriately randomised and controlled studies that will generate high-quality unbiased and generalisable evidence to ascertain whether or not auditory perceptual training has a clinically relevant effect on tinnitus. PMID:20668974

Evaluation of DNA mixtures from database search.

PubMed

Chung, Yuk-Ka; Hu, Yue-Qing; Fung, Wing K

2010-03-01

With the aim of bridging the gap between DNA mixture analysis and DNA database search, a novel approach is proposed to evaluate the forensic evidence of DNA mixtures when the suspect is identified by the search of a database of DNA profiles. General formulae are developed for the calculation of the likelihood ratio for a two-person mixture under general situations including multiple matches and imperfect evidence. The influence of the prior probabilities on the weight of evidence under the scenario of multiple matches is demonstrated by a numerical example based on Hong Kong data. Our approach is shown to be capable of presenting the forensic evidence of DNA mixtures in a comprehensive way when the suspect is identified through database search.

Faster sequence homology searches by clustering subsequences.

PubMed

Suzuki, Shuji; Kakuta, Masanori; Ishida, Takashi; Akiyama, Yutaka

2015-04-15

Sequence homology searches are used in various fields. New sequencing technologies produce huge amounts of sequence data, which continuously increase the size of sequence databases. As a result, homology searches require large amounts of computational time, especially for metagenomic analysis. We developed a fast homology search method based on database subsequence clustering, and implemented it as GHOSTZ. This method clusters similar subsequences from a database to perform an efficient seed search and ungapped extension by reducing alignment candidates based on triangle inequality. The database subsequence clustering technique achieved an ∼2-fold increase in speed without a large decrease in search sensitivity. When we measured with metagenomic data, GHOSTZ is ∼2.2-2.8 times faster than RAPSearch and is ∼185-261 times faster than BLASTX. The source code is freely available for download at http://www.bi.cs.titech.ac.jp/ghostz/ akiyama@cs.titech.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Search Filter Precision Can Be Improved By NOTing Out Irrelevant Content

PubMed Central

Wilczynski, Nancy L.; McKibbon, K. Ann; Haynes, R. Brian

2011-01-01

Background: Most methodologic search filters developed for use in large electronic databases such as MEDLINE have low precision. One method that has been proposed but not tested for improving precision is NOTing out irrelevant content. Objective: To determine if search filter precision can be improved by NOTing out the text words and index terms assigned to those articles that are retrieved but are off-target. Design: Analytic survey. Methods: NOTing out unique terms in off-target articles and testing search filter performance in the Clinical Hedges Database. Main Outcome Measures: Sensitivity, specificity, precision and number needed to read (NNR). Results: For all purpose categories (diagnosis, prognosis and etiology) except treatment and for all databases (MEDLINE, EMBASE, CINAHL and PsycINFO), constructing search filters that NOTed out irrelevant content resulted in substantive improvements in NNR (over four-fold for some purpose categories and databases). Conclusion: Search filter precision can be improved by NOTing out irrelevant content. PMID:22195215

System for Performing Single Query Searches of Heterogeneous and Dispersed Databases

NASA Technical Reports Server (NTRS)

Maluf, David A. (Inventor); Okimura, Takeshi (Inventor); Gurram, Mohana M. (Inventor); Tran, Vu Hoang (Inventor); Knight, Christopher D. (Inventor); Trinh, Anh Ngoc (Inventor)

2017-01-01

The present invention is a distributed computer system of heterogeneous databases joined in an information grid and configured with an Application Programming Interface hardware which includes a search engine component for performing user-structured queries on multiple heterogeneous databases in real time. This invention reduces overhead associated with the impedance mismatch that commonly occurs in heterogeneous database queries.

The Use of AJAX in Searching a Bibliographic Database: A Case Study of the Italian Biblioteche Oggi Database

ERIC Educational Resources Information Center

Cavaleri, Piero

2008-01-01

Purpose: The purpose of this paper is to describe the use of AJAX for searching the Biblioteche Oggi database of bibliographic records. Design/methodology/approach: The paper is a demonstration of how bibliographic database single page interfaces allow the implementation of more user-friendly features for social and collaborative tasks. Findings:…

On the predictability of protein database search complexity and its relevance to optimization of distributed searches.

PubMed

Deciu, Cosmin; Sun, Jun; Wall, Mark A

2007-09-01

We discuss several aspects related to load balancing of database search jobs in a distributed computing environment, such as Linux cluster. Load balancing is a technique for making the most of multiple computational resources, which is particularly relevant in environments in which the usage of such resources is very high. The particular case of the Sequest program is considered here, but the general methodology should apply to any similar database search program. We show how the runtimes for Sequest searches of tandem mass spectral data can be predicted from profiles of previous representative searches, and how this information can be used for better load balancing of novel data. A well-known heuristic load balancing method is shown to be applicable to this problem, and its performance is analyzed for a variety of search parameters.

Archive of mass spectral data files on recordable CD-ROMs and creation and maintenance of a searchable computerized database.

PubMed

Amick, G D

1999-01-01

A database containing names of mass spectral data files generated in a forensic toxicology laboratory and two Microsoft Visual Basic programs to maintain and search this database is described. The data files (approximately 0.5 KB/each) were collected from six mass spectrometers during routine casework. Data files were archived on 650 MB (74 min) recordable CD-ROMs. Each recordable CD-ROM was given a unique name, and its list of data file names was placed into the database. The present manuscript describes the use of search and maintenance programs for searching and routine upkeep of the database and creation of CD-ROMs for archiving of data files.

Description of 'REQUEST-KYUSHYU' for KYUKEICHO regional data base

NASA Astrophysics Data System (ADS)

Takimoto, Shin'ichi

Kyushu Economic Research Association (a foundational juridical person) initiated the regional database services, ' REQUEST-Kyushu ' recently. It is the full scale databases compiled based on the information and know-hows which the Association has accumulated over forty years. It covers the regional information database for journal and newspaper articles, and statistical information database for economic statistics. As to the former database it is searched on a personal computer and then a search result (original text) is sent through a facsimile. As to the latter, it is also searched on a personal computer where the data is processed, edited or downloaded. This paper describes characteristics, content and the system outline of 'REQUEST-Kyushu'.

OrChem - An open source chemistry search engine for Oracle®

PubMed Central

2009-01-01

Background Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Results Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. Availability OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net. PMID:20298521

The Human Transcript Database: A Catalogue of Full Length cDNA Inserts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bouckk John; Michael McLeod; Kim Worley

1999-09-10

The BCM Search Launcher provided improved access to web-based sequence analysis services during the granting period and beyond. The Search Launcher web site grouped analysis procedures by function and provided default parameters that provided reasonable search results for most applications. For instance, most queries were automatically masked for repeat sequences prior to sequence database searches to avoid spurious matches. In addition to the web-based access and arrangements that were made using the functions easier, the BCM Search Launcher provided unique value-added applications like the BEAUTY sequence database search tool that combined information about protein domains and sequence database search resultsmore » to give an enhanced, more complete picture of the reliability and relative value of the information reported. This enhanced search tool made evaluating search results more straight-forward and consistent. Some of the favorite features of the web site are the sequence utilities and the batch client functionality that allows processing of multiple samples from the command line interface. One measure of the success of the BCM Search Launcher is the number of sites that have adopted the models first developed on the site. The graphic display on the BLAST search from the NCBI web site is one such outgrowth, as is the display of protein domain search results within BLAST search results, and the design of the Biology Workbench application. The logs of usage and comments from users confirm the great utility of this resource.« less

Does non-invasive brain stimulation modify hand dexterity? Protocol for a systematic review and meta-analysis.

PubMed

O'Brien, Anthony Terrence; Torrealba Acosta, Gabriel; Huerta, Rodrigo; Thibaut, Aurore

2017-06-22

Dexterity is described as coordinated hand and finger movement for precision tasks. It is essential for day-to-day activities like computer use, writing or buttoning a shirt. Integrity of brain motor networks is crucial to properly execute these fine hand tasks. When these networks are damaged, interventions to enhance recovery are frequently accompanied by unwanted side effects or limited in their effect. Non-invasive brain stimulation (NIBS) are postulated to target affected motor areas and improve hand motor function with few side effects. However, the results across studies vary, and the current literature does not allow us to draw clear conclusions on the use of NIBS to promote hand function recovery. Therefore, we developed a protocol for a systematic review and meta-analysis on the effects of different NIBS technologies on dexterity in diverse populations. This study will potentially help future evidence-based research and guidelines that use these NIBS technologies for recovering hand dexterity. This protocol will compare the effects of active versus sham NIBS on precise hand activity. Records will be obtained by searching relevant databases. Included articles will be randomised clinical trials in adults, testing the therapeutic effects of NIBS on continuous dexterity data. Records will be studied for risk of bias. Narrative and quantitative synthesis will be done. No private health information is included; the study is not interventional. Ethical approval is not required. The results will be reported in a peer-review journal. PROSPERO International prospective register of systematic reviews registration number: CRD42016043809. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

The CIS Database: Occupational Health and Safety Information Online.

ERIC Educational Resources Information Center

Siegel, Herbert; Scurr, Erica

1985-01-01

Describes document acquisition, selection, indexing, and abstracting and discusses online searching of the CIS database, an online system produced by the International Occupational Safety and Health Information Centre. This database comprehensively covers information in the field of occupational health and safety. Sample searches and search…

Federated Search Tools in Fusion Centers: Bridging Databases in the Information Sharing Environment

DTIC Science & Technology

2012-09-01

considerable variation in how fusion centers plan for, gather requirements, select and acquire federated search tools to bridge disparate databases...centers, when considering integrating federated search tools; by evaluating the importance of the planning, requirements gathering, selection and...acquisition processes for integrating federated search tools; by acknowledging the challenges faced by some fusion centers during these integration processes

Quality of audio-assisted versus video-assisted dispatcher-instructed bystander cardiopulmonary resuscitation: A systematic review and meta-analysis.

PubMed

Lin, Yu-You; Chiang, Wen-Chu; Hsieh, Ming-Ju; Sun, Jen-Tang; Chang, Yi-Chung; Ma, Matthew Huei-Ming

2018-02-01

This study aimed to conduct a systematic review and meta-analysis comparing the effect of video-assistance and audio-assistance on quality of dispatcher-instructed cardiopulmonary resuscitation (DI-CPR) for bystanders. Five databases were searched, including PubMed, Cochrane library, Embase, Scopus and NIH clinical trial, to find randomized control trials published before June 2017. Qualitative analysis and meta-analysis were undertaken to examine the difference between the quality of video-instructed and audio-instructed dispatcher-instructed bystander CPR. The database search yielded 929 records, resulting in the inclusion of 9 relevant articles in this study. Of these, 6 were included in the meta-analysis. Initiation of chest compressions was slower in the video-instructed group than in the audio-instructed group (median delay 31.5 s; 95% CI: 10.94-52.09). The difference in the number of chest compressions per minute between the groups was 19.9 (95% CI: 10.50-29.38) with significantly faster compressions in the video-instructed group than in the audio-instructed group (104.8 vs. 80.6). The odds ratio (OR) for correct hand positioning was 0.8 (95% CI: 0.53-1.30) when comparing the audio-instructed and video-instructed groups. The differences in chest compression depth (mm) and time to first ventilation (seconds) between the video-instructed group and audio-instructed group were 1.6 mm (95% CI: -8.75, 5.55) and 7.5 s (95% CI: -56.84, 71.80), respectively. Video-instructed DI-CPR significantly improved the chest compression rate compared to the audio-instructed method, and a trend for correctness of hand position was also observed. However, this method caused a delay in the commencement of bystander-initiated CPR in the simulation setting. Copyright © 2017 Elsevier B.V. All rights reserved.

Physiotherapy and occupational therapy interventions for people with benign joint hypermobility syndrome: a systematic review of clinical trials.

PubMed

Smith, Toby O; Bacon, Holly; Jerman, Emma; Easton, Vicky; Armon, Kate; Poland, Fiona; Macgregor, Alex J

2014-01-01

This study assessed the literature to determine the efficacy and effectiveness of physiotherapy and occupational therapy interventions in the treatment of people with benign joint hypermobility syndrome (BJHS). Published literature databases including: AMED, CINAHL, MEDLINE, EMBASE, PubMed and the Cochrane Library, in addition to unpublished databases and trial registries were searched to October 2012. All clinical trials comparing the clinical outcomes of Occupational Therapy and Physiotherapy interventions compared to non-treatment or control intervention for people with BJHS were included. Of the 126 search results, 3 clinical studies satisfied the eligibility criteria. The data provides limited support for the use of wrist/hand splints for school children. While there is some support for exercise-based intervention, there is insufficient research to determine the optimal mode, frequency, dosage or type of exercise which should be delivered. The current evidence-base surrounding Occupational Therapy and Physiotherapy in the management of BJHS is limited in size and quality. There is insufficient research exploring the clinical outcomes of a number of interventions including sensory integration, positioning and posture management and education. Longer term, rigorous multi-centre randomised controlled trials are warranted to begin to assess the clinical and cost-effectiveness of interventions for children and adults with BJHS. Implications for Rehabilitation There is an evidence-base to support clinician's use of proprioceptive-based exercises in adults, and either tailored or generalised physiotherapy regimes for children with BJHS. Clinicians should be cautious when considering the prescription of hand/wrist splints for school age children with BJHS, based on the current research. Until further multi-centre trials are conducted assessing the clinical and cost-effectiveness of interventions for children and adult with BJHS, clinical decision-making should be based on theoretical rather than evidence-based grounds for this population.

Two- versus four-handed techniques for endonasal resection of orbital apex tumors.

PubMed

Craig, John R; Lee, John Y K; Petrov, Dmitriy; Mehta, Sonul; Palmer, James N; Adappa, Nithin D

2015-01-01

Open versus endonasal resection of orbital apex (OA) tumors is generally based on tumor size, location, and pathology. For endonasal resection, two- and four-handed techniques have been reported, but whether one technique is more optimal based on these tumor features has not been evaluated. To determine whether two- versus four-handed techniques result in better outcomes after endoscopic resection of OA tumors, and whether either technique is better suited for intra- versus extraconal location and for benign versus malignant pathology. A retrospective review of all expanded endonasal approaches for OA tumors was performed at a single institution from 2009 to 2013. A PubMed database search was also performed to review series published on endonasal OA tumor resection. Across all the cases reviewed, the following data were recorded: two- versus four-handed techniques, intra- versus extraconal tumor location, and benign versus malignant pathology. The relationship between these variables and resection extent was analyzed by the Fisher exact test. Postoperative visual status and complications were also reviewed. Ten cases from the institution and 94 cases from 17 publications were reviewed. Both two- and four-handed techniques were used to resect extra- and intraconal OA tumors, for both benign and malignant pathology. Four-handed techniques included a purely endonasal approach and a combined endonasal-orbital approach. On univariate analysis, the strongest predictor of complete resection was benign pathology (p = 0.005). No significant difference was found between the extent of resection and a two- versus a four-handed technique. Visual status was improved or unchanged in 94% of cases, and other complications were rare. Benign tumors that involve the medial extraconal and posterior inferomedial intraconal OA can be treated by either two- or four-handed endonasal techniques. Selecting two- versus four-handed techniques and endonasal versus endonasal-orbital four-handed techniques depends mainly on surgeons' experience. Endonasal approaches for malignant OA tumors are less likely to result in complete resection.

A review of issues and concerns of family members of adult burn survivors.

PubMed

Sundara, Diana C

2011-01-01

The purpose of this review is to synthesize what is known about the issues and concerns of families of adult burn survivors from research and clinical articles written between 1973 and 2009. Electronic database searching, ancestry searching, and electronic hand searching were performed to identify relevant articles. Seventeen research studies and 14 clinical articles were identified. Families are often in crisis immediately after the injury. This crisis involves strong emotions, some of which may persist over time. Throughout the course of hospitalization, family issues include worries about their loved one's physical appearance, logistical concerns, and the transition to home. For partners, role changes and sexual concerns may be of particular importance. Extended family, friends, the burn team, and other families affected by a burn injury are important sources of support for family members. Few studies have been conducted beyond the time of hospitalization. Clinical articles have identified issues not present in the research literature. Further research is needed that focuses more closely on families and their experiences both in and out of the hospital. Implications for burn care providers based on the findings of this review are discussed.

The impact of polygamy on women's mental health: a systematic review.

PubMed

Shepard, L D

2013-03-01

Aims. The purpose of this systematic review is to identify and appraise the present state of prevalence research on the mental health of polygynous women, or plural wives, and to summarize its implications for future research and social work practice. Methods. PsycInfo (1967 to November 2011) and Medline (1985 to November 2011) databases, systematic bibliography hand-searches, personal communication with a leading expert, and gray literature searching were applied in a systematic literature search of the prevalence of mental-health issues in polygynous women compared to monogamous women. Twenty-two studies meeting eligibility criteria were identified. Study characteristics, methods and findings were systematically extracted and appraised for quality. Results. The identified studies are of mixed methodological quality, but generally suggest a more significant prevalence of mental-health issues in polygynous women compared to monogamous women. Individual studies report a higher prevalence of somatization, depression, anxiety, hostility, psychoticism and psychiatric disorder in polygynous wives as well as reduced life and marital satisfaction, problematic family functioning and low self-esteem. Conclusions. The current state of the research reveals with moderate confidence, a more significant prevalence of mental-health issues in polygynous women as compared to monogamous women. Implications for practice and research are indicated.

Training socially responsive health care graduates: is service learning an effective educational approach?

PubMed

Mc Menamin, Ruth; Mc Grath, Margaret; Cantillon, Peter; Mac Farlane, Anne

2014-04-01

Health care educators strive to train graduates who are socially responsive and can act as "change agents" for communities they serve. Service learning (SL) is increasingly being used to teach the social aspects of health care and develop students' social responsiveness. However, the effectiveness of SL as an educational intervention has not been established. To assess the evidence for the effectiveness of SL. Seven electronic databases were searched up to 2012 and included all articles on SL for pre-professional health care students. Hand searching was also conducted. A total of 1485 articles were identified, 53 fulfilled the search and quality appraisal criteria and were reviewed across six domains of potential SL effects: (i) personal and interpersonal development; (ii) understanding and applying knowledge; (iii) engagement, curiosity and reflective practice; (iv) critical thinking; (v) perspective transformation and (vi) citizenship. While SL experiences appear highly valued by educators and students the effectiveness of SL remains unclear. SL is different from other forms of experiential learning because it explicitly aims to establish reciprocity between all partners and increase students' social responsiveness. Impact studies based on the interpretative paradigm, aligned with the principles of social accountability and including all stakeholder perspectives are necessary.

Effects of technical editing in biomedical journals: a systematic review.

PubMed

Wager, Elizabeth; Middleton, Philippa

2002-06-05

Technical editing supposedly improves the accuracy and clarity of journal articles. We examined evidence of its effects on research reports in biomedical journals. Subset of a systematic review using Cochrane methods, searching MEDLINE, EMBASE, and other databases from earliest entries to February 2000 by using inclusive search terms; hand searching relevant journals. We selected comparative studies of the effects of editorial processes on original research articles between acceptance and publication in biomedical journals. Two reviewers assessed each study and performed independent data extraction. The 11 studies on technical editing indicate that it improves the readability of articles slightly (as measured by Gunning Fog and Flesch reading ease scores), may improve other aspects of their quality, can increase the accuracy of references and quotations, and raises the quality of abstracts. Supplying authors with abstract preparation instructions had no discernible effect. Considering the time and resources devoted to technical editing, remarkably little is know about its effects or the effects of imposing different house styles. Studies performed at 3 journals employing relatively large numbers of professional technical editors suggest that their editorial processes are associated with increases in readability and quality of articles, but these findings may not be generalizable to other journals.

A Scoping Review of Maternal and Child Health Clinicians Attitudes, Beliefs, Practice, Training and Perceived Self-Competence in Environmental Health.

PubMed

Massaquoi, Lamin Daddy; Edwards, Nancy Christine

2015-12-10

Clinicians regularly assess, diagnose and manage illnesses which are directly or indirectly linked to environmental exposures. Yet, various studies have identified gaps in environmental assessment in routine clinical practice. This review assessed clinicians' environmental health practices, attitudes and beliefs, and competencies and training. Relevant articles were sought using a systematic search strategy using five databases, grey literature and a hand search. Search strategies and protocols were developed using tailored mesh terms and keywords. 43 out of 11,291 articles were eligible for inclusion. Clinicians' attitudes and beliefs towards environmental health and routine clinical practice were generally positive, with most clinicians believing that environmental hazards affect human health. However, with the exception of tobacco smoke exposure, environmental health assessment was infrequently part of routine clinical practice. Clinicians' self-competence in environmental assessment was reported to be inadequate. Major challenges were the time required to complete an assessment, inadequate training and concerns about negative patients' responses. Clinicians have strong positive attitudes and beliefs about the importance of environmental health assessments. However, more concerted and robust strategies will be needed to support clinicians in assuming their assessment and counselling roles related to a wider range of environmental hazards.

How to locate and appraise qualitative research in complementary and alternative medicine

PubMed Central

2013-01-01

Background The aim of this publication is to present a case study of how to locate and appraise qualitative studies for the conduct of a meta-ethnography in the field of complementary and alternative medicine (CAM). CAM is commonly associated with individualized medicine. However, one established scientific approach to the individual, qualitative research, thus far has been explicitly used very rarely. This article demonstrates a case example of how qualitative research in the field of CAM studies was identified and critically appraised. Methods Several search terms and techniques were tested for the identification and appraisal of qualitative CAM research in the conduct of a meta-ethnography. Sixty-seven electronic databases were searched for the identification of qualitative CAM trials, including CAM databases, nursing, nutrition, psychological, social, medical databases, the Cochrane Library and DIMDI. Results 9578 citations were screened, 223 articles met the pre-specified inclusion criteria, 63 full text publications were reviewed, 38 articles were appraised qualitatively and 30 articles were included. The search began with PubMed, yielding 87% of the included publications of all databases with few additional relevant findings in the specific databases. CINHAL and DIMDI also revealed a high number of precise hits. Although CAMbase and CAM-QUEST® focus on CAM research only, almost no hits of qualitative trials were found there. Searching with broad text terms was the most effective search strategy in all databases. Conclusions This publication presents a case study on how to locate and appraise qualitative studies in the field of CAM. The example shows that the literature search for qualitative studies in the field of CAM is most effective when the search is begun in PubMed followed by CINHAL or DIMDI using broad text terms. Exclusive CAM databases delivered no additional findings to locate qualitative CAM studies. PMID:23731997

How to locate and appraise qualitative research in complementary and alternative medicine.

PubMed

Franzel, Brigitte; Schwiegershausen, Martina; Heusser, Peter; Berger, Bettina

2013-06-03

The aim of this publication is to present a case study of how to locate and appraise qualitative studies for the conduct of a meta-ethnography in the field of complementary and alternative medicine (CAM). CAM is commonly associated with individualized medicine. However, one established scientific approach to the individual, qualitative research, thus far has been explicitly used very rarely. This article demonstrates a case example of how qualitative research in the field of CAM studies was identified and critically appraised. Several search terms and techniques were tested for the identification and appraisal of qualitative CAM research in the conduct of a meta-ethnography. Sixty-seven electronic databases were searched for the identification of qualitative CAM trials, including CAM databases, nursing, nutrition, psychological, social, medical databases, the Cochrane Library and DIMDI. 9578 citations were screened, 223 articles met the pre-specified inclusion criteria, 63 full text publications were reviewed, 38 articles were appraised qualitatively and 30 articles were included. The search began with PubMed, yielding 87% of the included publications of all databases with few additional relevant findings in the specific databases. CINHAL and DIMDI also revealed a high number of precise hits. Although CAMbase and CAM-QUEST® focus on CAM research only, almost no hits of qualitative trials were found there. Searching with broad text terms was the most effective search strategy in all databases. This publication presents a case study on how to locate and appraise qualitative studies in the field of CAM. The example shows that the literature search for qualitative studies in the field of CAM is most effective when the search is begun in PubMed followed by CINHAL or DIMDI using broad text terms. Exclusive CAM databases delivered no additional findings to locate qualitative CAM studies.

Hand-held computer operating system program for collection of resident experience data.

PubMed

Malan, T K; Haffner, W H; Armstrong, A Y; Satin, A J

2000-11-01

To describe a system for recording resident experience involving hand-held computers with the Palm Operating System (3 Com, Inc., Santa Clara, CA). Hand-held personal computers (PCs) are popular, easy to use, inexpensive, portable, and can share data among other operating systems. Residents in our program carry individual hand-held database computers to record Residency Review Committee (RRC) reportable patient encounters. Each resident's data is transferred to a single central relational database compatible with Microsoft Access (Microsoft Corporation, Redmond, WA). Patient data entry and subsequent transfer to a central database is accomplished with commercially available software that requires minimal computer expertise to implement and maintain. The central database can then be used for statistical analysis or to create required RRC resident experience reports. As a result, the data collection and transfer process takes less time for residents and program director alike, than paper-based or central computer-based systems. The system of collecting resident encounter data using hand-held computers with the Palm Operating System is easy to use, relatively inexpensive, accurate, and secure. The user-friendly system provides prompt, complete, and accurate data, enhancing the education of residents while facilitating the job of the program director.

Association Between Alcohol Sports Sponsorship and Consumption: A Systematic Review.

PubMed

Brown, Katherine

2016-11-01

Concerns have been raised about the impact of alcohol sports sponsorship on harmful consumption, with some countries banning this practice or considering a ban. We review evidence on the relationship between exposure to alcohol sports sponsorship and alcohol consumption. Search of electronic databases (PubMed, Cochrane Library, Google Scholar and International Alcohol Information Database) supplemented by hand searches of references and conference proceedings to locate studies providing data on the impact of exposure to alcohol sports sponsorship and outcomes relating to alcohol consumption. Seven studies met inclusion criteria, presenting data on 12,760 participants from Australia, New Zealand, the UK, Germany, Italy, Netherlands and Poland. All studies report positive associations between exposure to alcohol sports sponsorship and self-reported alcohol consumption, but the statistical significance of results varies. Two studies found indirect exposure to alcohol sports sponsorship was associated with increased levels of drinking amongst schoolchildren, and five studies found a positive association between direct alcohol sports sponsorship and hazardous drinking amongst adult sportspeople. These findings corroborate the results of previous systematic reviews that reported a positive association between exposure to alcohol marketing and alcohol consumption. The relationship between alcohol sports sponsorship and increased drinking amongst schoolchildren will concern policymakers. Further research into the effectiveness of restrictions on alcohol sports sponsorship in reducing harmful drinking is required. © The Author 2016. Medical Council on Alcohol and Oxford University Press.

Effective nonvaccine interventions to be considered alongside human papilloma virus vaccine delivery.

PubMed

Hindin, Michelle J; Bloem, Paul; Ferguson, Jane

2015-01-01

World Health Organization recommends that girls, ages 9-13 years, get the human papilloma virus (HPV) vaccine. Global Alliance for Vaccines Initiative, which provides low-cost vaccine to eligible countries, requires that an additional intervention to be offered alongside the vaccine. We systematically searched and assessed the published literature in lower- and middle-income countries to identify effective interventions. We conducted systematic searches of four databases: PubMed, EMBASE, Global Index Medicus Regional Databases, and Cochrane Reviews for effective adolescent health interventions that could be delivered with the HPV vaccine in the following areas: (1) iron and folic acid supplementation (iron alone or with folic acid); (2) voucher delivery and cash transfer programs; (3) hand washing and soap provision; (4) vision screening; (5) promotion of physical activity/exercise; (6) menstrual hygiene education; (7) sexual and reproductive health education; (8) human immunodeficiency virus prevention activities; and (9) condom promotion, condom use skill building, and demonstration. We found limited evidence of consistent positive impact. Iron supplementation reduced iron-deficiency anemia and raised serum ferritin levels. Promotion of physical activity lowered blood pressure and reduced weight gain. Sexual and reproductive health and human immunodeficiency virus interventions improved adolescent communication with adults but did not influence behavioral outcomes. Countries should consider locally relevant and proven interventions to be offered alongside the HPV vaccine. Copyright © 2015 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Biomedical Requirements for High Productivity Computing Systems

DTIC Science & Technology

2005-04-01

server at http://www.ncbi.nlm.nih.gov/BLAST/. There are many variants of BLAST, including: 1. BLASTN - Compares a DNA query to a DNA database. Searches ...database (3 reading frames from each strand of the DNA) searching . 13 4. TBLASTN - Compares a protein query to a DNA database, in the 6 possible...the molecular during this phase. After eliminating molecules that could not match the query , an atom-by-atom search for the molecules in conducted

Multi-Database Searching in the Behavioral Sciences--Part I: Basic Techniques and Core Databases.

ERIC Educational Resources Information Center

Angier, Jennifer J.; Epstein, Barbara A.

1980-01-01

Outlines practical searching techniques in seven core behavioral science databases accessing psychological literature: Psychological Abstracts, Social Science Citation Index, Biosis, Medline, Excerpta Medica, Sociological Abstracts, ERIC. Use of individual files is discussed and their relative strengths/weaknesses are compared. Appended is a list…

Subject Specific Databases: A Powerful Research Tool

ERIC Educational Resources Information Center

Young, Terrence E., Jr.

2004-01-01

Subject specific databases, or vortals (vertical portals), are databases that provide highly detailed research information on a particular topic. They are the smallest, most focused search tools on the Internet and, in recent years, they've been on the rise. Currently, more of the so-called "mainstream" search engines, subject directories, and…

Subject Retrieval from Full-Text Databases in the Humanities

ERIC Educational Resources Information Center

East, John W.

2007-01-01

This paper examines the problems involved in subject retrieval from full-text databases of secondary materials in the humanities. Ten such databases were studied and their search functionality evaluated, focusing on factors such as Boolean operators, document surrogates, limiting by subject area, proximity operators, phrase searching, wildcards,…

A Framework for Cloudy Model Optimization and Database Storage

NASA Astrophysics Data System (ADS)

Calvén, Emilia; Helton, Andrew; Sankrit, Ravi

2018-01-01

We present a framework for producing Cloudy photoionization models of the nebular emission from novae ejecta and storing a subset of the results in SQL database format for later usage. The database can be searched for models best fitting observed spectral line ratios. Additionally, the framework includes an optimization feature that can be used in tandem with the database to search for and improve on models by creating new Cloudy models while, varying the parameters. The database search and optimization can be used to explore the structures of nebulae by deriving their properties from the best-fit models. The goal is to provide the community with a large database of Cloudy photoionization models, generated from parameters reflecting conditions within novae ejecta, that can be easily fitted to observed spectral lines; either by directly accessing the database using the framework code or by usage of a website specifically made for this purpose.

Effectiveness of Motivational Interviewing Interventions for Adolescent Substance Use Behavior Change: A Meta-Analytic Review

ERIC Educational Resources Information Center

Jensen, Chad D.; Cushing, Christopher C.; Aylward, Brandon S.; Craig, James T.; Sorell, Danielle M.; Steele, Ric G.

2011-01-01

Objective: This study was designed to quantitatively evaluate the effectiveness of motivational interviewing (MI) interventions for adolescent substance use behavior change. Method: Literature searches of electronic databases were undertaken in addition to manual reference searches of identified review articles. Databases searched include…

The LAILAPS search engine: a feature model for relevance ranking in life science databases.

PubMed

Lange, Matthias; Spies, Karl; Colmsee, Christian; Flemming, Steffen; Klapperstück, Matthias; Scholz, Uwe

2010-03-25

Efficient and effective information retrieval in life sciences is one of the most pressing challenge in bioinformatics. The incredible growth of life science databases to a vast network of interconnected information systems is to the same extent a big challenge and a great chance for life science research. The knowledge found in the Web, in particular in life-science databases, are a valuable major resource. In order to bring it to the scientist desktop, it is essential to have well performing search engines. Thereby, not the response time nor the number of results is important. The most crucial factor for millions of query results is the relevance ranking. In this paper, we present a feature model for relevance ranking in life science databases and its implementation in the LAILAPS search engine. Motivated by the observation of user behavior during their inspection of search engine result, we condensed a set of 9 relevance discriminating features. These features are intuitively used by scientists, who briefly screen database entries for potential relevance. The features are both sufficient to estimate the potential relevance, and efficiently quantifiable. The derivation of a relevance prediction function that computes the relevance from this features constitutes a regression problem. To solve this problem, we used artificial neural networks that have been trained with a reference set of relevant database entries for 19 protein queries. Supporting a flexible text index and a simple data import format, this concepts are implemented in the LAILAPS search engine. It can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. LAILAPS is publicly available for SWISSPROT data at http://lailaps.ipk-gatersleben.de.

Digital hand atlas for web-based bone age assessment: system design and implementation

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente

2000-04-01

A frequently used assessment method of skeletal age is atlas matching by a radiological examination of a hand image against a small set of Greulich-Pyle patterns of normal standards. The method however can lead to significant deviation in age assessment, due to a variety of observers with different levels of training. The Greulich-Pyle atlas based on middle upper class white populations in the 1950s, is also not fully applicable for children of today, especially regarding the standard development in other racial groups. In this paper, we present our system design and initial implementation of a digital hand atlas and computer-aided diagnostic (CAD) system for Web-based bone age assessment. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. The system consists of a hand atlas database, a CAD module and a Java-based Web user interface. The atlas database is based on a large set of clinically normal hand images of diverse ethnic groups. The Java-based Web user interface allows users to interact with the hand image database form browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, is then extracted and compared with patterns from the atlas database to assess the bone age.

77 FR 6535 - Notice of Intent To Seek Approval To Collect Information

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-08

... information from participants: Contact information, affiliation, and database searching experience... and fax numbers, and email address. Six questions are asked regarding: database searching experience...

Preconception risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease.

PubMed

Hussein, Norita; Weng, Stephen F; Kai, Joe; Kleijnen, Jos; Qureshi, Nadeem

2015-08-12

Globally, about five per cent of children are born with congenital or genetic disorders. The most common autosomal recessive conditions are thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease, with higher carrier rates in specific patient populations. Identifying and counselling couples at genetic risk of the conditions before pregnancy enables them to make fully informed reproductive decisions, with some of these choices not being available if genetic counselling is only offered in an antenatal setting. To assess the effectiveness of systematic preconception genetic risk assessment to improve reproductive outcomes in women and their partners who are identified as carriers of thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease in healthcare settings when compared to usual care. We searched the Cochrane Cystic Fibrosis and Genetic Disorders Group's Trials Registers. In addition, we searched for all relevant trials from 1970 (or the date at which the database was first available if after 1970) to date using electronic databases (MEDLINE, Embase, CINAHL, PsycINFO), clinical trial databases (National Institutes of Health, Clinical Trials Search portal of the World Health Organization, metaRegister of controlled clinical trials), and hand searching of key journals and conference abstract books from 1998 to date (European Journal of Human Genetics, Genetics in Medicine, Journal of Community Genetics). We also searched the reference lists of relevant articles, reviews and guidelines and also contacted subject experts in the field to request any unpublished or other published trials.Date of latest search of the registers: 25 June 2015.Date of latest search of all other sources: 10 December 2014. Any randomised or quasi-randomised control trials (published or unpublished) comparing reproductive outcomes of systematic preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease when compared to usual care. We identified 19 papers, describing 13 unique trials which were potentially eligible for inclusion in the review. However, after assessment, no randomised controlled trials of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease were found. No randomised controlled trials of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease were found. As no randomised controlled trials of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis, or Tay-Sachs disease were found for inclusion in this review, the research evidence for current policy recommendations is limited to non-randomised studies.Information from well-designed, adequately powered, randomised trials is desirable in order to make more robust recommendations for practice. However, such trials must also consider the legal, ethical, and cultural barriers to implementation of preconception genetic risk assessment.

Searching mixed DNA profiles directly against profile databases.

PubMed

Bright, Jo-Anne; Taylor, Duncan; Curran, James; Buckleton, John

2014-03-01

DNA databases have revolutionised forensic science. They are a powerful investigative tool as they have the potential to identify persons of interest in criminal investigations. Routinely, a DNA profile generated from a crime sample could only be searched for in a database of individuals if the stain was from single contributor (single source) or if a contributor could unambiguously be determined from a mixed DNA profile. This meant that a significant number of samples were unsuitable for database searching. The advent of continuous methods for the interpretation of DNA profiles offers an advanced way to draw inferential power from the considerable investment made in DNA databases. Using these methods, each profile on the database may be considered a possible contributor to a mixture and a likelihood ratio (LR) can be formed. Those profiles which produce a sufficiently large LR can serve as an investigative lead. In this paper empirical studies are described to determine what constitutes a large LR. We investigate the effect on a database search of complex mixed DNA profiles with contributors in equal proportions with dropout as a consideration, and also the effect of an incorrect assignment of the number of contributors to a profile. In addition, we give, as a demonstration of the method, the results using two crime samples that were previously unsuitable for database comparison. We show that effective management of the selection of samples for searching and the interpretation of the output can be highly informative. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases

PubMed Central

Lee, Taein; Cheng, Chun-Huai; Ficklin, Stephen; Yu, Jing; Humann, Jodi; Main, Dorrie

2017-01-01

Abstract Tripal is an open-source database platform primarily used for development of genomic, genetic and breeding databases. We report here on the release of the Chado Loader, Chado Data Display and Chado Search modules to extend the functionality of the core Tripal modules. These new extension modules provide additional tools for (1) data loading, (2) customized visualization and (3) advanced search functions for supported data types such as organism, marker, QTL/Mendelian Trait Loci, germplasm, map, project, phenotype, genotype and their respective metadata. The Chado Loader module provides data collection templates in Excel with defined metadata and data loaders with front end forms. The Chado Data Display module contains tools to visualize each data type and the metadata which can be used as is or customized as desired. The Chado Search module provides search and download functionality for the supported data types. Also included are the tools to visualize map and species summary. The use of materialized views in the Chado Search module enables better performance as well as flexibility of data modeling in Chado, allowing existing Tripal databases with different metadata types to utilize the module. These Tripal Extension modules are implemented in the Genome Database for Rosaceae (rosaceae.org), CottonGen (cottongen.org), Citrus Genome Database (citrusgenomedb.org), Genome Database for Vaccinium (vaccinium.org) and the Cool Season Food Legume Database (coolseasonfoodlegume.org). Database URL: https://www.citrusgenomedb.org/, https://www.coolseasonfoodlegume.org/, https://www.cottongen.org/, https://www.rosaceae.org/, https://www.vaccinium.org/

Difficulties and challenges associated with literature searches in operating room management, complete with recommendations.

PubMed

Wachtel, Ruth E; Dexter, Franklin

2013-12-01

The purpose of this article is to teach operating room managers, financial analysts, and those with a limited knowledge of search engines, including PubMed, how to locate articles they need in the areas of operating room and anesthesia group management. Many physicians are unaware of current literature in their field and evidence-based practices. The most common source of information is colleagues. Many people making management decisions do not read published scientific articles. Databases such as PubMed are available to search for such articles. Other databases, such as citation indices and Google Scholar, can be used to uncover additional articles. Nevertheless, most people who do not know how to use these databases are reluctant to utilize help resources when they do not know how to accomplish a task. Most people are especially reluctant to use on-line help files. Help files and search databases are often difficult to use because they have been designed for users already familiar with the field. The help files and databases have specialized vocabularies unique to the application. MeSH terms in PubMed are not useful alternatives for operating room management, an important limitation, because MeSH is the default when search terms are entered in PubMed. Librarians or those trained in informatics can be valuable assets for searching unusual databases, but they must possess the domain knowledge relative to the subject they are searching. The search methods we review are especially important when the subject area (e.g., anesthesia group management) is so specific that only 1 or 2 articles address the topic of interest. The materials are presented broadly enough that the reader can extrapolate the findings to other areas of clinical and management issues in anesthesiology.

HBVPathDB: a database of HBV infection-related molecular interaction network.

PubMed

Zhang, Yi; Bo, Xiao-Chen; Yang, Jing; Wang, Sheng-Qi

2005-03-21

To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus' and host's genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection. The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML). We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1 050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at http://www.bio-inf.net/HBVPathDB/HBV/. The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.

Multi-source and ontology-based retrieval engine for maize mutant phenotypes

PubMed Central

Green, Jason M.; Harnsomburana, Jaturon; Schaeffer, Mary L.; Lawrence, Carolyn J.; Shyu, Chi-Ren

2011-01-01

Model Organism Databases, including the various plant genome databases, collect and enable access to massive amounts of heterogeneous information, including sequence data, gene product information, images of mutant phenotypes, etc, as well as textual descriptions of many of these entities. While a variety of basic browsing and search capabilities are available to allow researchers to query and peruse the names and attributes of phenotypic data, next-generation search mechanisms that allow querying and ranking of text descriptions are much less common. In addition, the plant community needs an innovative way to leverage the existing links in these databases to search groups of text descriptions simultaneously. Furthermore, though much time and effort have been afforded to the development of plant-related ontologies, the knowledge embedded in these ontologies remains largely unused in available plant search mechanisms. Addressing these issues, we have developed a unique search engine for mutant phenotypes from MaizeGDB. This advanced search mechanism integrates various text description sources in MaizeGDB to aid a user in retrieving desired mutant phenotype information. Currently, descriptions of mutant phenotypes, loci and gene products are utilized collectively for each search, though expansion of the search mechanism to include other sources is straightforward. The retrieval engine, to our knowledge, is the first engine to exploit the content and structure of available domain ontologies, currently the Plant and Gene Ontologies, to expand and enrich retrieval results in major plant genomic databases. Database URL: http:www.PhenomicsWorld.org/QBTA.php PMID:21558151

BLAST and FASTA similarity searching for multiple sequence alignment.

PubMed

Pearson, William R

2014-01-01

BLAST, FASTA, and other similarity searching programs seek to identify homologous proteins and DNA sequences based on excess sequence similarity. If two sequences share much more similarity than expected by chance, the simplest explanation for the excess similarity is common ancestry-homology. The most effective similarity searches compare protein sequences, rather than DNA sequences, for sequences that encode proteins, and use expectation values, rather than percent identity, to infer homology. The BLAST and FASTA packages of sequence comparison programs provide programs for comparing protein and DNA sequences to protein databases (the most sensitive searches). Protein and translated-DNA comparisons to protein databases routinely allow evolutionary look back times from 1 to 2 billion years; DNA:DNA searches are 5-10-fold less sensitive. BLAST and FASTA can be run on popular web sites, but can also be downloaded and installed on local computers. With local installation, target databases can be customized for the sequence data being characterized. With today's very large protein databases, search sensitivity can also be improved by searching smaller comprehensive databases, for example, a complete protein set from an evolutionarily neighboring model organism. By default, BLAST and FASTA use scoring strategies target for distant evolutionary relationships; for comparisons involving short domains or queries, or searches that seek relatively close homologs (e.g. mouse-human), shallower scoring matrices will be more effective. Both BLAST and FASTA provide very accurate statistical estimates, which can be used to reliably identify protein sequences that diverged more than 2 billion years ago.

Concentrations of indoor pollutants database: User's manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1992-05-01

This manual describes the computer-based database on indoor air pollutants. This comprehensive database alloys helps utility personnel perform rapid searches on literature related to indoor air pollutants. Besides general information, it provides guidance for finding specific information on concentrations of indoor air pollutants. The manual includes information on installing and using the database as well as a tutorial to assist the user in becoming familiar with the procedures involved in doing bibliographic and summary section searches. The manual demonstrates how to search for information by going through a series of questions that provide search parameters such as pollutants type, year,more » building type, keywords (from a specific list), country, geographic region, author's last name, and title. As more and more parameters are specified, the list of references found in the data search becomes smaller and more specific to the user's needs. Appendixes list types of information that can be input into the database when making a request. The CIP database allows individual utilities to obtain information on indoor air quality based on building types and other factors in their own service territory. This information is useful for utilities with concerns about indoor air quality and the control of indoor air pollutants. The CIP database itself is distributed by the Electric Power Software Center and runs on IBM PC-compatible computers.« less

Concentrations of indoor pollutants database: User`s manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1992-05-01

This manual describes the computer-based database on indoor air pollutants. This comprehensive database alloys helps utility personnel perform rapid searches on literature related to indoor air pollutants. Besides general information, it provides guidance for finding specific information on concentrations of indoor air pollutants. The manual includes information on installing and using the database as well as a tutorial to assist the user in becoming familiar with the procedures involved in doing bibliographic and summary section searches. The manual demonstrates how to search for information by going through a series of questions that provide search parameters such as pollutants type, year,more » building type, keywords (from a specific list), country, geographic region, author`s last name, and title. As more and more parameters are specified, the list of references found in the data search becomes smaller and more specific to the user`s needs. Appendixes list types of information that can be input into the database when making a request. The CIP database allows individual utilities to obtain information on indoor air quality based on building types and other factors in their own service territory. This information is useful for utilities with concerns about indoor air quality and the control of indoor air pollutants. The CIP database itself is distributed by the Electric Power Software Center and runs on IBM PC-compatible computers.« less

Clinically significant drug-drug interactions involving opioid analgesics used for pain treatment in patients with cancer: a systematic review.

PubMed

Kotlinska-Lemieszek, Aleksandra; Klepstad, Pål; Haugen, Dagny Faksvåg

2015-01-01

Opioids are the most frequently used drugs to treat pain in cancer patients. In some patients, however, opioids can cause adverse effects and drug-drug interactions. No advice concerning the combination of opioids and other drugs is given in the current European guidelines. To identify studies that report clinically significant drug-drug interactions involving opioids used for pain treatment in adult cancer patients. Systematic review with searches in Embase, MEDLINE, and Cochrane Central Register of Controlled Trials from the start of the databases (Embase from 1980) through January 2014. In addition, reference lists of relevant full-text papers were hand-searched. Of 901 retrieved papers, 112 were considered as potentially eligible. After full-text reading, 17 were included in the final analysis, together with 15 papers identified through hand-searching of reference lists. All of the 32 included publications were case reports or case series. Clinical manifestations of drug-drug interactions involving opioids were grouped as follows: 1) sedation and respiratory depression, 2) other central nervous system symptoms, 3) impairment of pain control and/or opioid withdrawal, and 4) other symptoms. The most common mechanisms eliciting drug-drug interactions were alteration of opioid metabolism by inhibiting the activity of cytochrome P450 3A4 and pharmacodynamic interactions due to the combined effect on opioid, dopaminergic, cholinergic, and serotonergic activity in the central nervous system. Evidence for drug-drug interactions associated with opioids used for pain treatment in cancer patients is very limited. Still, the cases identified in this systematic review give some important suggestions for clinical practice. Physicians prescribing opioids should recognize the risk of drug-drug interactions and if possible avoid polypharmacy.

Dorsal scapular nerve neuropathy: a narrative review of the literature

PubMed Central

Muir, Brad

2017-01-01

Objective The purpose of this paper is to elucidate this little known cause of upper back pain through a narrative review of the literature and to discuss the possible role of the dorsal scapular nerve (DSN) in the etiopathology of other similar diagnoses in this area including cervicogenic dorsalgia (CD), notalgia paresthetica (NP), SICK scapula and a posterolateral arm pain pattern. Background Dorsal scapular nerve (DSN) neuropathy has been a rarely thought of differential diagnosis for mid scapular, upper to mid back and costovertebral pain. These are common conditions presenting to chiropractic, physiotherapy, massage therapy and medical offices. Methods The methods used to gather articles for this paper included: searching electronic databases; and hand searching relevant references from journal articles and textbook chapters. Results One hundred-fourteen articles were retrieved. After removing duplicates, there were 57 articles of which 29 were retrieved. There were 26 articles and textbook chapters retrieved by hand searching equaling 55 articles retrieved of which 47 relevant articles were used in this report. Discussion The anatomy, pathway and function of the dorsal scapular nerve can be varied and exceptionally rarely may include a sensory component. The signs and symptoms, therefore, may include pain, atrophy, scapular winging, and dysesthesia. The mechanism of injury to the DSN is also quite varied ranging from postural to overuse in overhead work and sport. Other conditions in this area, including CD, NP, SICK scapula and a posterolateral arm pain pattern bear a striking resemblance to DSN neuropathy. Conclusion DSN neuropathy should be included in the list of common differential diagnoses of upper and mid-thoracic pain, stiffness, dysesthesia and dysfunction. The study also brings forward interesting connections between DSN neuropathy, CD, NP, SICK scapula and a posterolateral arm pain pattern. PMID:28928496

Personal hand gel for improved hand hygiene compliance on the regional anesthesia team.

PubMed

Parks, Colby L; Schroeder, Kristopher M; Galgon, Richard E

2015-12-01

Hand hygiene reduces healthcare-associated infections, and several recent publications have examined hand hygiene in the perioperative period. Our institution's policy is to perform hand hygiene before and after patient contact. However, observation suggests poor compliance. This is a retrospective review of a quality improvement database showing the effect of personal gel dispensers on perioperative hand hygiene compliance on a regional anesthesia team. Healthcare providers assigned to the Acute Pain Service were observed for compliance with hand hygiene policy during a quality improvement initiative. Provider type and compliance were prospectively recorded in a database. Team members were then given a personal gel dispensing device and again observed for compliance. We have retrospectively reviewed this database to determine the effects of this intervention. Of the 307 encounters observed, 146 were prior to implementing personal gel dispensers. Compliance was 34%. Pre- and post-patient contact compliances were 23 and 43%, respectively. For 161 encounters after individual gel dispensers were provided, compliance was 63%. Pre- and post-patient contact compliances were 53 and 72%, respectively. Improvement in overall compliance from 34 to 63% was significant. On the Acute Pain Service, compliance with hand hygiene policy improves when individual sanitation gel dispensing devices are worn on the person.

DRUMS: a human disease related unique gene mutation search engine.

PubMed

Li, Zuofeng; Liu, Xingnan; Wen, Jingran; Xu, Ye; Zhao, Xin; Li, Xuan; Liu, Lei; Zhang, Xiaoyan

2011-10-01

With the completion of the human genome project and the development of new methods for gene variant detection, the integration of mutation data and its phenotypic consequences has become more important than ever. Among all available resources, locus-specific databases (LSDBs) curate one or more specific genes' mutation data along with high-quality phenotypes. Although some genotype-phenotype data from LSDB have been integrated into central databases little effort has been made to integrate all these data by a search engine approach. In this work, we have developed disease related unique gene mutation search engine (DRUMS), a search engine for human disease related unique gene mutation as a convenient tool for biologists or physicians to retrieve gene variant and related phenotype information. Gene variant and phenotype information were stored in a gene-centred relational database. Moreover, the relationships between mutations and diseases were indexed by the uniform resource identifier from LSDB, or another central database. By querying DRUMS, users can access the most popular mutation databases under one interface. DRUMS could be treated as a domain specific search engine. By using web crawling, indexing, and searching technologies, it provides a competitively efficient interface for searching and retrieving mutation data and their relationships to diseases. The present system is freely accessible at http://www.scbit.org/glif/new/drums/index.html. © 2011 Wiley-Liss, Inc.

A Systematic Review of Outcome Measurements and Quality of Studies Evaluating Fixed Tooth-Supported Restorations

PubMed Central

Patel, Devangkumar Rajnikant; O'Brien, Tim; Petrie, Aviva; Petridis, Haralampos

2014-01-01

Purpose The purpose of this systematic review was to review clinical studies of fixed tooth-supported prostheses, and to assess the quality of evidence with an emphasis on the assessment of the reporting of outcome measurements. Multiple hypotheses were generated to compare the effect of study type on different outcome modifiers and to compare the quality of publications before and after January 2005. Materials and Methods An electronic search was conducted using specific databases (MEDLINE via Ovid, EMBASE via Ovid, Cochrane Library) through July 2012. This was complemented by hand searching the past 10 years of issues of the Journal of Oral Rehabilitation, Journal of Prosthetic Dentistry, Journal of Prosthodontics, and the International Journal of Prosthodontics. All experimental and observational clinical studies evaluating survival, success, failure, and complications of tooth-supported extracoronal fixed partial dentures, crowns, and onlays were included. No restrictions on age or follow-up time were placed. Results The electronic search generated 14,869 papers, of which 206 papers were included for full-text review. Hand-searching added 23 papers. Inclusion criteria were met by 182 papers and were included for the review. The majority were retrospective studies. Only 8 (4.4%) were randomized controlled trials. The majority of the studies measured survival and failure, and few studies recorded data on success; however, more than 60% of the studies failed to define survival, success, and failure. Many studies did not use any standardized criteria for assessment of the quality of the restorations and, when standardized criteria were used, they were modified, thereby not allowing for comparisons with other studies. There was an increase of 21.8% in the number of studies evaluating outcome measurements of all-ceramic restorations in past 8 years. Conclusions Prosthodontic literature presents with a reduced percentage of RCTs compared to other disciplines in dentistry. The overall quality of recording prosthodontic outcome measurements has not improved greatly in the past 8 years. PMID:24947268

Cone beam computed tomography in implant dentistry: a systematic review focusing on guidelines, indications, and radiation dose risks.

PubMed

Bornstein, Michael M; Scarfe, William C; Vaughn, Vida M; Jacobs, Reinhilde

2014-01-01

The aim of the paper is to identify, review, analyze, and summarize available evidence in three areas on the use of cross-sectional imaging, specifically maxillofacial cone beam computed tomography (CBCT) in pre- and postoperative dental implant therapy: (1) Available clinical use guidelines, (2) indications and contraindications for use, and (3) assessment of associated radiation dose risk. Three focused questions were developed to address the aims. A systematic literature review was performed using a PICO-based search strategy based on MeSH key words specific to each focused question of English-language publications indexed in the MEDLINE database retrospectively from October 31, 2012. These results were supplemented by a hand search and gray literature search. Twelve publications were identified providing guidelines for the use of cross-sectional radiography, particularly CBCT imaging, for the pre- and/or postoperative assessment of potential dental implant sites. The publications discovered by the PICO strategy (43 articles), hand (12), and gray literature searches (1) for the second focus question regarding indications and contraindications for CBCT use in implant dentistry were either cohort or case-controlled studies. For the third question on the assessment of associated radiation dose risk, a total of 22 articles were included. Publication characteristics and themes were summarized in tabular format. The reported indications for CBCT use in implant dentistry vary from preoperative analysis regarding specific anatomic considerations, site development using grafts, and computer-assisted treatment planning to postoperative evaluation focusing on complications due to damage of neurovascular structures. Effective doses for different CBCT devices exhibit a wide range with the lowest dose being almost 100 times less than the highest dose. Significant dose reduction can be achieved by adjusting operating parameters, including exposure factors and reducing the field of view (FOV) to the actual region of interest.

Accelerating Information Retrieval from Profile Hidden Markov Model Databases.

PubMed

Tamimi, Ahmad; Ashhab, Yaqoub; Tamimi, Hashem

2016-01-01

Profile Hidden Markov Model (Profile-HMM) is an efficient statistical approach to represent protein families. Currently, several databases maintain valuable protein sequence information as profile-HMMs. There is an increasing interest to improve the efficiency of searching Profile-HMM databases to detect sequence-profile or profile-profile homology. However, most efforts to enhance searching efficiency have been focusing on improving the alignment algorithms. Although the performance of these algorithms is fairly acceptable, the growing size of these databases, as well as the increasing demand for using batch query searching approach, are strong motivations that call for further enhancement of information retrieval from profile-HMM databases. This work presents a heuristic method to accelerate the current profile-HMM homology searching approaches. The method works by cluster-based remodeling of the database to reduce the search space, rather than focusing on the alignment algorithms. Using different clustering techniques, 4284 TIGRFAMs profiles were clustered based on their similarities. A representative for each cluster was assigned. To enhance sensitivity, we proposed an extended step that allows overlapping among clusters. A validation benchmark of 6000 randomly selected protein sequences was used to query the clustered profiles. To evaluate the efficiency of our approach, speed and recall values were measured and compared with the sequential search approach. Using hierarchical, k-means, and connected component clustering techniques followed by the extended overlapping step, we obtained an average reduction in time of 41%, and an average recall of 96%. Our results demonstrate that representation of profile-HMMs using a clustering-based approach can significantly accelerate data retrieval from profile-HMM databases.

THGS: a web-based database of Transmembrane Helices in Genome Sequences

PubMed Central

Fernando, S. A.; Selvarani, P.; Das, Soma; Kumar, Ch. Kiran; Mondal, Sukanta; Ramakumar, S.; Sekar, K.

2004-01-01

Transmembrane Helices in Genome Sequences (THGS) is an interactive web-based database, developed to search the transmembrane helices in the user-interested gene sequences available in the Genome Database (GDB). The proposed database has provision to search sequence motifs in transmembrane and globular proteins. In addition, the motif can be searched in the other sequence databases (Swiss-Prot and PIR) or in the macromolecular structure database, Protein Data Bank (PDB). Further, the 3D structure of the corresponding queried motif, if it is available in the solved protein structures deposited in the Protein Data Bank, can also be visualized using the widely used graphics package RASMOL. All the sequence databases used in the present work are updated frequently and hence the results produced are up to date. The database THGS is freely available via the world wide web and can be accessed at http://pranag.physics.iisc.ernet.in/thgs/ or http://144.16.71.10/thgs/. PMID:14681375

Data-driven indexing mechanism for the recognition of polyhedral objects

NASA Astrophysics Data System (ADS)

McLean, Stewart; Horan, Peter; Caelli, Terry M.

1992-02-01

This paper is concerned with the problem of searching large model databases. To date, most object recognition systems have concentrated on the problem of matching using simple searching algorithms. This is quite acceptable when the number of object models is small. However, in the future, general purpose computer vision systems will be required to recognize hundreds or perhaps thousands of objects and, in such circumstances, efficient searching algorithms will be needed. The problem of searching a large model database is one which must be addressed if future computer vision systems are to be at all effective. In this paper we present a method we call data-driven feature-indexed hypothesis generation as one solution to the problem of searching large model databases.

Optimal search strategies for detecting health services research studies in MEDLINE

PubMed Central

Wilczynski, Nancy L.; Haynes, R. Brian; Lavis, John N.; Ramkissoonsingh, Ravi; Arnold-Oatley, Alexandra E.

2004-01-01

Background Evidence from health services research (HSR) is currently thinly spread through many journals, making it difficult for health services researchers, managers and policy-makers to find research on clinical practice guidelines and the appropriateness, process, outcomes, cost and economics of health care services. We undertook to develop and test search terms to retrieve from the MEDLINE database HSR articles meeting minimum quality standards. Methods The retrieval performance of 7445 methodologic search terms and phrases in MEDLINE (the test) were compared with a hand search of the literature (the gold standard) for each issue of 68 journal titles for the year 2000 (a total of 25 936 articles). We determined sensitivity, specificity and precision (the positive predictive value) of the MEDLINE search strategies. Results A majority of the articles that were classified as outcome assessment, but fewer than half of those in the other categories, were considered methodologically acceptable (no methodologic criteria were applied for cost studies). Combining individual search terms to maximize sensitivity, while keeping specificity at 50% or more, led to sensitivities in the range of 88.1% to 100% for several categories (specificities ranged from 52.9% to 97.4%). When terms were combined to maximize specificity while keeping sensitivity at 50% or more, specificities of 88.8% to 99.8% were achieved. When terms were combined to maximize sensitivity and specificity while minimizing the differences between the 2 measurements, most strategies for HSR categories achieved sensitivity and specificity of at least 80%. Interpretation Sensitive and specific search strategies were validated for retrieval of HSR literature from MEDLINE. These strategies have been made available for public use by the US National Library of Medicine at www.nlm.nih.gov/nichsr/hedges/search.html. PMID:15534310

Novel LOVD databases for hereditary breast cancer and colorectal cancer genes in the Chinese population.

PubMed

Pan, Min; Cong, Peikuan; Wang, Yue; Lin, Changsong; Yuan, Ying; Dong, Jian; Banerjee, Santasree; Zhang, Tao; Chen, Yanling; Zhang, Ting; Chen, Mingqing; Hu, Peter; Zheng, Shu; Zhang, Jin; Qi, Ming

2011-12-01

The Human Variome Project (HVP) is an international consortium of clinicians, geneticists, and researchers from over 30 countries, aiming to facilitate the establishment and maintenance of standards, systems, and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The HVP-China Node will build new and supplement existing databases of genetic diseases. As the first effort, we have created a novel variant database of BRCA1 and BRCA2, mismatch repair genes (MMR), and APC genes for breast cancer, Lynch syndrome, and familial adenomatous polyposis (FAP), respectively, in the Chinese population using the Leiden Open Variation Database (LOVD) format. We searched PubMed and some Chinese search engines to collect all the variants of these genes in the Chinese population that have already been detected and reported. There are some differences in the gene variants between the Chinese population and that of other ethnicities. The database is available online at http://www.genomed.org/LOVD/. Our database will appear to users who survey other LOVD databases (e.g., by Google search, or by NCBI GeneTests search). Remote submissions are accepted, and the information is updated monthly. © 2011 Wiley Periodicals, Inc.

Comparison of CINAHL, EMBASE, and MEDLINE databases for the nurse researcher.

PubMed

Burnham, J; Shearer, B

1993-01-01

The purpose of this research was to determine which of three databases, CINAHL, EMBASE or MEDLINE, should be accessed when researching nursing topics. The three databases were searched for citations on topics selected by three nurse researchers and the results were compared. For the search of nursing care literature on a medical condition, it was helpful to search both CINAHL and MEDLINE. CINAHL provided the majority of relevant articles for the second search, on computers and privacy, but inclusion of MEDLINE and EMBASE enhanced retrieval somewhat. The search on substance abuse in pregnancy, not restricted to nursing literature, retrieved better results when searching both MEDLINE and EMBASE. Due to the nature and distribution of the nursing literature, it is especially important for the searcher to understand and respond to the focus of the researcher.

Choosing a Database for Social Work: A Comparison of Social Work Abstracts and Social Service Abstracts

ERIC Educational Resources Information Center

Flatley, Robert K.; Lilla, Rick; Widner, Jack

2007-01-01

This study compared Social Work Abstracts and Social Services Abstracts databases in terms of indexing, journal coverage, and searches. The authors interviewed editors, analyzed journal coverage, and compared searches. It was determined that the databases complement one another more than compete. The authors conclude with some considerations.

The Philip Morris Information Network: A Library Database on an In-House Timesharing System.

ERIC Educational Resources Information Center

DeBardeleben, Marian Z.; And Others

1983-01-01

Outlines a database constructed at Philip Morris Research Center Library which encompasses holdings and circulation and acquisitions records for all items in the library. Host computer (DECSYSTEM-2060), software (BASIC), database design, search methodology, cataloging, and accessibility are noted; sample search, circ-in profile, end user profiles,…

How Many People Search the ERIC Database Each Day?

ERIC Educational Resources Information Center

Rudner, Lawrence

This study estimated the number of people searching the ERIC database each day. The Educational Resources Information Center (ERIC) is a national information system designed to provide ready access to an extensive body of education-related literature. Federal funds traditionally have paid for the development of the database, but not the…

FirstSearch and NetFirst--Web and Dial-up Access: Plus Ca Change, Plus C'est la Meme Chose?

ERIC Educational Resources Information Center

Koehler, Wallace; Mincey, Danielle

1996-01-01

Compares and evaluates the differences between OCLC's dial-up and World Wide Web FirstSearch access methods and their interfaces with the underlying databases. Also examines NetFirst, OCLC's new Internet catalog, the only Internet tracking database from a "traditional" database service. (Author/PEN)

Ocean Drilling Program: Web Site Access Statistics

Science.gov Websites

and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main See statistics for JOIDES members. See statistics for Janus database. 1997 October November December accessible only on www-odp.tamu.edu. ** End of ODP, start of IODP. Privacy Policy ODP | Search | Database

Digging Deeper: The Deep Web.

ERIC Educational Resources Information Center

Turner, Laura

2001-01-01

Focuses on the Deep Web, defined as Web content in searchable databases of the type that can be found only by direct query. Discusses the problems of indexing; inability to find information not indexed in the search engine's database; and metasearch engines. Describes 10 sites created to access online databases or directly search them. Lists ways…

A practical approach for inexpensive searches of radiology report databases.

PubMed

Desjardins, Benoit; Hamilton, R Curtis

2007-06-01

We present a method to perform full text searches of radiology reports for the large number of departments that do not have this ability as part of their radiology or hospital information system. A tool written in Microsoft Access (front-end) has been designed to search a server (back-end) containing the indexed backup weekly copy of the full relational database extracted from a radiology information system (RIS). This front end-/back-end approach has been implemented in a large academic radiology department, and is used for teaching, research and administrative purposes. The weekly second backup of the 80 GB, 4 million record RIS database takes 2 hours. Further indexing of the exported radiology reports takes 6 hours. Individual searches of the indexed database typically take less than 1 minute on the indexed database and 30-60 minutes on the nonindexed database. Guidelines to properly address privacy and institutional review board issues are closely followed by all users. This method has potential to improve teaching, research, and administrative programs within radiology departments that cannot afford more expensive technology.

Decision making in family medicine: randomized trial of the effects of the InfoClinique and Trip database search engines.

PubMed

Labrecque, Michel; Ratté, Stéphane; Frémont, Pierre; Cauchon, Michel; Ouellet, Jérôme; Hogg, William; McGowan, Jessie; Gagnon, Marie-Pierre; Njoya, Merlin; Légaré, France

2013-10-01

To compare the ability of users of 2 medical search engines, InfoClinique and the Trip database, to provide correct answers to clinical questions and to explore the perceived effects of the tools on the clinical decision-making process. Randomized trial. Three family medicine units of the family medicine program of the Faculty of Medicine at Laval University in Quebec city, Que. Fifteen second-year family medicine residents. Residents generated 30 structured questions about therapy or preventive treatment (2 questions per resident) based on clinical encounters. Using an Internet platform designed for the trial, each resident answered 20 of these questions (their own 2, plus 18 of the questions formulated by other residents, selected randomly) before and after searching for information with 1 of the 2 search engines. For each question, 5 residents were randomly assigned to begin their search with InfoClinique and 5 with the Trip database. The ability of residents to provide correct answers to clinical questions using the search engines, as determined by third-party evaluation. After answering each question, participants completed a questionnaire to assess their perception of the engine's effect on the decision-making process in clinical practice. Of 300 possible pairs of answers (1 answer before and 1 after the initial search), 254 (85%) were produced by 14 residents. Of these, 132 (52%) and 122 (48%) pairs of answers concerned questions that had been assigned an initial search with InfoClinique and the Trip database, respectively. Both engines produced an important and similar absolute increase in the proportion of correct answers after searching (26% to 62% for InfoClinique, for an increase of 36%; 24% to 63% for the Trip database, for an increase of 39%; P = .68). For all 30 clinical questions, at least 1 resident produced the correct answer after searching with either search engine. The mean (SD) time of the initial search for each question was 23.5 (7.6) minutes with InfoClinique and 22.3 (7.8) minutes with the Trip database (P = .30). Participants' perceptions of each engine's effect on the decision-making process were very positive and similar for both search engines. Family medicine residents' ability to provide correct answers to clinical questions increased dramatically and similarly with the use of both InfoClinique and the Trip database. These tools have strong potential to increase the quality of medical care.

SymDex: increasing the efficiency of chemical fingerprint similarity searches for comparing large chemical libraries by using query set indexing.

PubMed

Tai, David; Fang, Jianwen

2012-08-27

The large sizes of today's chemical databases require efficient algorithms to perform similarity searches. It can be very time consuming to compare two large chemical databases. This paper seeks to build upon existing research efforts by describing a novel strategy for accelerating existing search algorithms for comparing large chemical collections. The quest for efficiency has focused on developing better indexing algorithms by creating heuristics for searching individual chemical against a chemical library by detecting and eliminating needless similarity calculations. For comparing two chemical collections, these algorithms simply execute searches for each chemical in the query set sequentially. The strategy presented in this paper achieves a speedup upon these algorithms by indexing the set of all query chemicals so redundant calculations that arise in the case of sequential searches are eliminated. We implement this novel algorithm by developing a similarity search program called Symmetric inDexing or SymDex. SymDex shows over a 232% maximum speedup compared to the state-of-the-art single query search algorithm over real data for various fingerprint lengths. Considerable speedup is even seen for batch searches where query set sizes are relatively small compared to typical database sizes. To the best of our knowledge, SymDex is the first search algorithm designed specifically for comparing chemical libraries. It can be adapted to most, if not all, existing indexing algorithms and shows potential for accelerating future similarity search algorithms for comparing chemical databases.

Vehicle-triggered video compression/decompression for fast and efficient searching in large video databases

NASA Astrophysics Data System (ADS)

Bulan, Orhan; Bernal, Edgar A.; Loce, Robert P.; Wu, Wencheng

2013-03-01

Video cameras are widely deployed along city streets, interstate highways, traffic lights, stop signs and toll booths by entities that perform traffic monitoring and law enforcement. The videos captured by these cameras are typically compressed and stored in large databases. Performing a rapid search for a specific vehicle within a large database of compressed videos is often required and can be a time-critical life or death situation. In this paper, we propose video compression and decompression algorithms that enable fast and efficient vehicle or, more generally, event searches in large video databases. The proposed algorithm selects reference frames (i.e., I-frames) based on a vehicle having been detected at a specified position within the scene being monitored while compressing a video sequence. A search for a specific vehicle in the compressed video stream is performed across the reference frames only, which does not require decompression of the full video sequence as in traditional search algorithms. Our experimental results on videos captured in a local road show that the proposed algorithm significantly reduces the search space (thus reducing time and computational resources) in vehicle search tasks within compressed video streams, particularly those captured in light traffic volume conditions.

A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

PubMed

Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

2010-08-01

The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

Modernized Techniques for Dealing with Quality Data and Derived Products

NASA Astrophysics Data System (ADS)

Neiswender, C.; Miller, S. P.; Clark, D.

2008-12-01

"I just want a picture of the ocean floor in this area" is expressed all too often by researchers, educators, and students in the marine geosciences. As more sophisticated systems are developed to handle data collection and processing, the demand for quality data, and standardized products continues to grow. Data management is an invisible bridge between science and researchers/educators. The SIOExplorer digital library presents more than 50 years of ocean-going research. Prior to publication, all data is checked for quality using standardized criterion developed for each data stream. Despite the evolution of data formats and processing systems, SIOExplorer continues to present derived products in well- established formats. Standardized products are published for each cruise, and include a cruise report, MGD77 merged data, multi-beam flipbook, and underway profiles. Creation of these products is made possible by processing scripts, which continue to change with ever-evolving data formats. We continue to explore the potential of database-enabled creation of standardized products, such as the metadata-rich MGD77 header file. Database-enabled, automated processing produces standards-compliant metadata for each data and derived product. Metadata facilitates discovery and interpretation of published products. This descriptive information is stored both in an ASCII file, and a searchable digital library database. SIOExplorer's underlying technology allows focused search and retrieval of data and products. For example, users can initiate a search of only multi-beam data, which includes data-specific parameters. This customization is made possible with a synthesis of database, XML, and PHP technology. The combination of standardized products and digital library technology puts quality data and derived products in the hands of scientists. Interoperable systems enable distribution these published resources using technology such as web services. By developing modernized strategies to deal with data, Scripps Institution of Oceanography is able to produce and distribute well-formed, and quality-tested derived products, which aid research, understanding, and education.

Yet More Visualized JAMSTEC Cruise and Dive Information

NASA Astrophysics Data System (ADS)

Tomiyama, T.; Hase, H.; Fukuda, K.; Saito, H.; Kayo, M.; Matsuda, S.; Azuma, S.

2014-12-01

Every year, JAMSTEC performs about a hundred of research cruises and numerous dive surveys using its research vessels and submersibles. JAMSTEC provides data and samples obtained during these cruises and dives to international users through a series of data sites on the Internet. The "DARWIN (http://www.godac.jamstec.go.jp/darwin/e)" data site disseminates cruise and dive information. On DARWIN, users can search interested cruises and dives with a combination search form or an interactive tree menu, and find lists of observation data as well as links to surrounding databases. Document catalog, physical sample databases, and visual archive of dive surveys (e. g. in http://www.godac.jamstec.go.jp/jmedia/portal/e) are directly accessible from the lists. In 2014, DARWIN experienced an update, which was arranged mainly for enabling on-demand data visualization. Using　login users' functions, users can put listed data items into the virtual basket and then trim, plot and download the data. The visualization tools help users to quickly grasp the quality and characteristics of observation data. Meanwhile, JAMSTEC launched a new data site named "JDIVES (http://www.godac.jamstec.go.jp/jdives/e)"　to visualize data and sample information obtained by dive surveys. JDIVES shows tracks of dive surveys on the "Google Earth Plugin" and diagrams of deep-sea environmental data such as temperature, salinity, and depth. Submersible camera images and links to associated databases are placed along the dive tracks. The JDVIES interface enables users to perform so-called virtual dive surveys, which can help users to understand local geometries of dive spots and geological settings of associated data and samples. It is not easy for individual researchers to organize a huge amount of information recovered from each cruise and dive. The improved visibility and accessibility of JAMSTEC databases are advantageous not only for second-hand users, but also for on-board researchers themselves.

DOE Research and Development Accomplishments Website Policies/Important

Science.gov Websites

Links RSS Archive Videos XML DOE R&D Accomplishments DOE R&D Accomplishments searchQuery × Find searchQuery x Find DOE R&D Acccomplishments Navigation dropdown arrow The Basics Stories Snapshots R&D Nuggets Database dropdown arrow Search Tag Cloud Browse Reports Database Help

Pre-Service Teachers' Use of Library Databases: Some Insights

ERIC Educational Resources Information Center

Lamb, Janeen; Howard, Sarah; Easey, Michael

2014-01-01

The aim of this study is to investigate if providing mathematics education pre-service teachers with animated library tutorials on library and database searches changes their searching practices. This study involved the completion of a survey by 138 students and seven individual interviews before and after library search demonstration videos were…

The present status and problems in document retrieval system : document input type retrieval system

NASA Astrophysics Data System (ADS)

Inagaki, Hirohito

The office-automation (OA) made many changes. Many documents were begun to maintained in an electronic filing system. Therefore, it is needed to establish efficient document retrieval system to extract useful information. Current document retrieval systems are using simple word-matching, syntactic-matching, semantic-matching to obtain high retrieval efficiency. On the other hand, the document retrieval systems using special hardware devices, such as ISSP, were developed for aiming high speed retrieval. Since these systems can accept a single sentence or keywords as input, it is difficult to explain searcher's request. We demonstrated document input type retrieval system, which can directly accept document as an input, and can search similar documents from document data-base.

Impact of systemic sclerosis oral manifestations on patients' health-related quality of life: a systematic review.

PubMed

Smirani, Rawen; Truchetet, Marie-Elise; Poursac, Nicolas; Naveau, Adrien; Schaeverbeke, Thierry; Devillard, Raphaël

2018-06-01

Oropharyngeal features are frequent and often understated in the treatment clinical guidelines of systemic sclerosis in spite of important consequences on comfort, esthetics, nutrition and daily life. The aim of this systematic review was to assess a correlation between the oropharyngeal manifestations of systemic sclerosis and patients' health-related quality of life. A systematic search was conducted using four databases [PubMed ® , Cochrane Database ® , Dentistry & Oral Sciences Source ® , and SCOPUS ® ] up to January 2018, according to the Preferred reporting items for systematic reviews and meta analyses. Grey literature and hand search were also included. Study selection, risk bias assessment (Newcastle-Ottawa scale) and data extraction were performed by two independent reviewers. The review protocol was registered on PROSPERO database with the code CRD42018085994. From 375 screened studies, 6 cross-sectional studies were included in the systematic review. The total number of patients included per study ranged from 84 to 178. These studies reported a statistically significant association between oropharyngeal manifestations of systemic sclerosis (mainly assessed by maximal mouth opening and the mouth handicap in systemic sclerosis scale) and an impaired quality of life (measured by different scales). Studies were unequal concerning risk of bias mostly because of low level of evidence, different recruiting sources of samples, and different scales to assess the quality of life. This systematic review demonstrates a correlation between oropharyngeal manifestations of systemic sclerosis and impaired quality of life, despite the low level of evidence of included studies. Large-scaled studies are needed to provide stronger evidence of this association. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Ocean Drilling Program: Mirror Sites

Science.gov Websites

Publication services and products Drilling services and tools Online Janus database Search the ODP/TAMU web information, see www.iodp-usio.org. ODP | Search | Database | Drilling | Publications | Science | Cruise Info

Ocean Drilling Program: TAMU Staff Directory

Science.gov Websites

products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main web site Employment Opportunities ODP | Search | Database | Drilling | Publications | Science | Cruise Info | Public

[A survey of the best bibliographic searching system in occupational medicine and discussion of its implementation].

PubMed

Inoue, J

1991-12-01

When occupational health personnel, especially occupational physicians search bibliographies, they usually have to search bibliographies by themselves. Also, if a library is not available because of the location of their work place, they might have to rely on online databases. Although there are many commercial databases in the world, people who seldom use them, will have problems with on-line searching, such as user-computer interface, keywords, and so on. The present study surveyed the best bibliographic searching system in the field of occupational medicine by questionnaire through the use of DIALOG OnDisc MEDLINE as a commercial database. In order to ascertain the problems involved in determining the best bibliographic searching system, a prototype bibliographic searching system was constructed and then evaluated. Finally, solutions for the problems were discussed. These led to the following conclusions: to construct the best bibliographic searching system at the present time, 1) a concept of micro-to-mainframe links (MML) is needed for the computer hardware network; 2) multi-lingual font standards and an excellent common user-computer interface are needed for the computer software; 3) a short course and education of database management systems, and support of personal information processing for retrieved data are necessary for the practical use of the system.

Search for third-generation scalar leptoquarks and heavy right-handed neutrinos in final states with two tau leptons and two jets in proton-proton collisions at $$ \\sqrt{s}=13 $$ TeV

DOE PAGES

Sirunyan, A. M.; Tumasyan, A.; Adam, W.; ...

2017-07-26

A search is performed for third-generation scalar leptoquarks and heavy right-handed neutrinos in events containing one electron or muon, one hadronically decaying τ lepton, and at least two jets, using amore » $$ \\sqrt{s}=13 $$ TeV pp collision data sample corresponding to an integrated luminosity of 12.9 fb$$^{-1}$$ collected with the CMS detector at the LHC in 2016. The number of observed events is found to be in agreement with the standard model prediction. A limit is set at 95% confidence level on the product of the leptoquark pair production cross section and β$$^{2}$$, where β is the branching fraction of leptoquark decay to a τ lepton and a bottom quark. Assuming β = 1, third-generation leptoquarks with masses below 850 GeV are excluded at 95% confidence level. An additional search based on the same event topology involves heavy right-handed neutrinos, N$$_{R}$$, and right-handed W bosons, W$$_{R}$$, arising in a left-right symmetric extension of the standard model. In this search, W$$_{R}$$ bosons are assumed to decay to a tau lepton and N$$_{R}$$ followed by the decay of the N$$_{R}$$ to a tau lepton and an off-shell W$$_{R}$$ boson. Assuming the mass of the right-handed neutrino to be half of the mass of the right-handed W boson, W$$_{R}$$ boson masses below 2.9 TeV are excluded at 95% confidence level. Lastly, these results improve on the limits from previous searches for third-generation leptoquarks and heavy right-handed neutrinos with τ leptons in the final state.« less

Search for third-generation scalar leptoquarks and heavy right-handed neutrinos in final states with two tau leptons and two jets in proton-proton collisions at $$ \\sqrt{s}=13 $$ TeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sirunyan, A. M.; Tumasyan, A.; Adam, W.

A search is performed for third-generation scalar leptoquarks and heavy right-handed neutrinos in events containing one electron or muon, one hadronically decaying τ lepton, and at least two jets, using amore » $$ \\sqrt{s}=13 $$ TeV pp collision data sample corresponding to an integrated luminosity of 12.9 fb$$^{-1}$$ collected with the CMS detector at the LHC in 2016. The number of observed events is found to be in agreement with the standard model prediction. A limit is set at 95% confidence level on the product of the leptoquark pair production cross section and β$$^{2}$$, where β is the branching fraction of leptoquark decay to a τ lepton and a bottom quark. Assuming β = 1, third-generation leptoquarks with masses below 850 GeV are excluded at 95% confidence level. An additional search based on the same event topology involves heavy right-handed neutrinos, N$$_{R}$$, and right-handed W bosons, W$$_{R}$$, arising in a left-right symmetric extension of the standard model. In this search, W$$_{R}$$ bosons are assumed to decay to a tau lepton and N$$_{R}$$ followed by the decay of the N$$_{R}$$ to a tau lepton and an off-shell W$$_{R}$$ boson. Assuming the mass of the right-handed neutrino to be half of the mass of the right-handed W boson, W$$_{R}$$ boson masses below 2.9 TeV are excluded at 95% confidence level. Lastly, these results improve on the limits from previous searches for third-generation leptoquarks and heavy right-handed neutrinos with τ leptons in the final state.« less

Identification of biomedical journals in Spain and Latin America.

PubMed

Bonfill, Xavier; Osorio, Dimelza; Posso, Margarita; Solà, Ivan; Rada, Gabriel; Torres, Ania; García Dieguez, Marcelo; Piña-Pozas, Maricela; Díaz-García, Luisa; Tristán, Mario; Gandarilla, Omar; Rincón-Valenzuela, David A; Martí, Arturo; Hidalgo, Ricardo; Simancas-Racines, Daniel; López, Luis; Correa, Ricardo; Rojas-De-Arias, Antonieta; Loza, César; Gianneo, Óscar; Pardo, Hector

2015-12-01

Journals in languages other than English that publish original clinical research are often not well covered in the main biomedical databases and therefore often not included in systematic reviews. This study aimed to identify Spanish language biomedical journals from Spain and Latin America and to describe their main features. Journals were identified in electronic databases, publishers' catalogues and local registries. Eligibility was determined by assessing data from these sources or the journals' websites, when available. A total of 2457 journals were initially identified; 1498 met inclusion criteria. Spain (27.3%), Mexico (16.0%), Argentina (15.1%) and Chile (11.9%) had the highest number of journals. Most (85.8%) are currently active; 87.8% have an ISSN. The median and mean length of publication were 22 and 29 years, respectively. A total of 66.0% were indexed in at least one database; 3.0% had an impact factor in 2012. A total of 845 journals had websites (56.4%), of which 700 (82.8%) were searchable and 681 (80.6%) free of charge. Most of the identified journals have no impact factor or are not indexed in any of the major databases. The list of identified biomedical journals can be a useful resource when conducting hand searching activities and identifying clinical trials that otherwise would not be retrieved. © 2015 Health Libraries Group.

Search for heavy neutrinos and bosons with right-handed couplings in proton-proton collisions at

NASA Astrophysics Data System (ADS)

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Fabjan, C.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Kiesenhofer, W.; Knünz, V.; Krammer, M.; Krätschmer, I.; Liko, D.; Mikulec, I.; Rabady, D.; Rahbaran, B.; Rohringer, H.; Schöfbeck, R.; Strauss, J.; Taurok, A.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; Bansal, M.; Bansal, S.; Cornelis, T.; De Wolf, E. A.; Janssen, X.; Knutsson, A.; Luyckx, S.; Ochesanu, S.; Roland, B.; Rougny, R.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Blekman, F.; Blyweert, S.; D'Hondt, J.; Daci, N.; Heracleous, N.; Keaveney, J.; Lowette, S.; Maes, M.; Olbrechts, A.; Python, Q.; Strom, D.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Onsem, G. P.; Villella, I.; Caillol, C.; Clerbaux, B.; De Lentdecker, G.; Dobur, D.; Favart, L.; Gay, A. P. R.; Grebenyuk, A.; Léonard, A.; Mohammadi, A.; Perniè, L.; Reis, T.; Seva, T.; Thomas, L.; Vander Velde, C.; Vanlaer, P.; Wang, J.; Adler, V.; Beernaert, K.; Benucci, L.; Cimmino, A.; Costantini, S.; Crucy, S.; Dildick, S.; Fagot, A.; Garcia, G.; Mccartin, J.; Ocampo Rios, A. A.; Ryckbosch, D.; Salva Diblen, S.; Sigamani, M.; Strobbe, N.; Thyssen, F.; Tytgat, M.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Beluffi, C.; Bruno, G.; Castello, R.; Caudron, A.; Ceard, L.; Da Silveira, G. G.; Delaere, C.; du Pree, T.; Favart, D.; Forthomme, L.; Giammanco, A.; Hollar, J.; Jez, P.; Komm, M.; Lemaitre, V.; Nuttens, C.; Pagano, D.; Perrini, L.; Pin, A.; Piotrzkowski, K.; Popov, A.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Vizan Garcia, J. M.; Beliy, N.; Caebergs, T.; Daubie, E.; Hammad, G. H.; Júnior, W. L. Aldá; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Pol, M. E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; De Jesus Damiao, D.; De Oliveira Martins, C.; Fonseca De Souza, S.; Malbouisson, H.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santaolalla, J.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Bernardes, C. A.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Aleksandrov, A.; Genchev, V.; Iaydjiev, P.; Marinov, A.; Piperov, S.; Rodozov, M.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Hadjiiska, R.; Kozhuharov, V.; Litov, L.; Pavlov, B.; Petkov, P.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Du, R.; Jiang, C. H.; Liang, D.; Liang, S.; Plestina, R.; Tao, J.; Wang, X.; Wang, Z.; Asawatangtrakuldee, C.; Ban, Y.; Guo, Y.; Li, Q.; Li, W.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Zhang, L.; Zou, W.; Avila, C.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; Gomez Moreno, B.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Polic, D.; Puljak, I.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Kadija, K.; Luetic, J.; Mekterovic, D.; Sudic, L.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Bodlak, M.; Finger, M.; Finger, M.; Assran, Y.; Elgammal, S.; Mahmoud, M. A.; Radi, A.; Kadastik, M.; Murumaa, M.; Raidal, M.; Tiko, A.; Eerola, P.; Fedi, G.; Voutilainen, M.; Härkönen, J.; Karimäki, V.; Kinnunen, R.; Kortelainen, M. J.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Peltola, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Baffioni, S.; Beaudette, F.; Busson, P.; Charlot, C.; Dahms, T.; Dalchenko, M.; Dobrzynski, L.; Filipovic, N.; Florent, A.; Granier de Cassagnac, R.; Mastrolorenzo, L.; Miné, P.; Mironov, C.; Naranjo, I. N.; Nguyen, M.; Ochando, C.; Paganini, P.; Salerno, R.; Sauvan, J. b.; Sirois, Y.; Veelken, C.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J.-M.; Chabert, E. C.; Collard, C.; Conte, E.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Goetzmann, C.; Le Bihan, A.-C.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Beaupere, N.; Boudoul, G.; Brochet, S.; Carrillo Montoya, C. A.; Chasserat, J.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fan, J.; Fay, J.; Gascon, S.; Gouzevitch, M.; Ille, B.; Kurca, T.; Lethuillier, M.; Mirabito, L.; Perries, S.; Ruiz Alvarez, J. D.; Sabes, D.; Sgandurra, L.; Sordini, V.; Vander Donckt, M.; Verdier, P.; Viret, S.; Xiao, H.; Bagaturia, I.; Autermann, C.; Beranek, S.; Bontenackels, M.; Edelhoff, M.; Feld, L.; Hindrichs, O.; Klein, K.; Ostapchuk, A.; Perieanu, A.; Raupach, F.; Sammet, J.; Schael, S.; Weber, H.; Wittmer, B.; Zhukov, V.; Ata, M.; Dietz-Laursonn, E.; Duchardt, D.; Erdmann, M.; Fischer, R.; Güth, A.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Klingebiel, D.; Knutzen, S.; Kreuzer, P.; Merschmeyer, M.; Meyer, A.; Millet, P.; Olschewski, M.; Padeken, K.; Papacz, P.; Reithler, H.; Schmitz, S. A.; Sonnenschein, L.; Teyssier, D.; Thüer, S.; Weber, M.; Cherepanov, V.; Erdogan, Y.; Flügge, G.; Geenen, H.; Geisler, M.; Haj Ahmad, W.; Hoehle, F.; Kargoll, B.; Kress, T.; Kuessel, Y.; Lingemann, J.; Nowack, A.; Nugent, I. M.; Perchalla, L.; Pooth, O.; Stahl, A.; Asin, I.; Bartosik, N.; Behr, J.; Behrenhoff, W.; Behrens, U.; Bell, A. J.; Bergholz, M.; Bethani, A.; Borras, K.; Burgmeier, A.; Cakir, A.; Calligaris, L.; Campbell, A.; Choudhury, S.; Costanza, F.; Diez Pardos, C.; Dooling, S.; Dorland, T.; Eckerlin, G.; Eckstein, D.; Eichhorn, T.; Flucke, G.; Garcia, J. Garay; Geiser, A.; Gunnellini, P.; Hauk, J.; Hellwig, G.; Hempel, M.; Horton, D.; Jung, H.; Kalogeropoulos, A.; Kasemann, M.; Katsas, P.; Kieseler, J.; Kleinwort, C.; Krücker, D.; Lange, W.; Leonard, J.; Lipka, K.; Lobanov, A.; Lohmann, W.; Lutz, B.; Mankel, R.; Marfin, I.; Melzer-Pellmann, I.-A.; Meyer, A. B.; Mnich, J.; Mussgiller, A.; Naumann-Emme, S.; Nayak, A.; Novgorodova, O.; Nowak, F.; Ntomari, E.; Perrey, H.; Pitzl, D.; Placakyte, R.; Raspereza, A.; Ribeiro Cipriano, P. M.; Ron, E.; Sahin, M. Ö.; Salfeld-Nebgen, J.; Saxena, P.; Schmidt, R.; Schoerner-Sadenius, T.; Schröder, M.; Seitz, C.; Spannagel, S.; Vargas Trevino, A. D. R.; Walsh, R.; Wissing, C.; Aldaya Martin, M.; Blobel, V.; Centis Vignali, M.; Draeger, A. r.; Erfle, J.; Garutti, E.; Goebel, K.; Görner, M.; Haller, J.; Hoffmann, M.; Höing, R. S.; Kirschenmann, H.; Klanner, R.; Kogler, R.; Lange, J.; Lapsien, T.; Lenz, T.; Marchesini, I.; Ott, J.; Peiffer, T.; Pietsch, N.; Pöhlsen, T.; Rathjens, D.; Sander, C.; Schettler, H.; Schleper, P.; Schlieckau, E.; Schmidt, A.; Seidel, M.; Sibille, J.; Sola, V.; Stadie, H.; Steinbrück, G.; Troendle, D.; Usai, E.; Vanelderen, L.; Barth, C.; Baus, C.; Berger, J.; Böser, C.; Butz, E.; Chwalek, T.; De Boer, W.; Descroix, A.; Dierlamm, A.; Feindt, M.; Frensch, F.; Giffels, M.; Hartmann, F.; Hauth, T.; Husemann, U.; Katkov, I.; Kornmayer, A.; Kuznetsova, E.; Lobelle Pardo, P.; Mozer, M. U.; Müller, Th.; Nürnberg, A.; Quast, G.; Rabbertz, K.; Ratnikov, F.; Röcker, S.; Simonis, H. J.; Stober, F. M.; Ulrich, R.; Wagner-Kuhr, J.; Wayand, S.; Weiler, T.; Wolf, R.; Anagnostou, G.; Daskalakis, G.; Geralis, T.; Giakoumopoulou, V. A.; Kyriakis, A.; Loukas, D.; Markou, A.; Markou, C.; Psallidas, A.; Topsis-Giotis, I.; Panagiotou, A.; Saoulidou, N.; Stiliaris, E.; Aslanoglou, X.; Evangelou, I.; Flouris, G.; Foudas, C.; Kokkas, P.; Manthos, N.; Papadopoulos, I.; Paradas, E.; Bencze, G.; Hajdu, C.; Hidas, P.; Horvath, D.; Sikler, F.; Veszpremi, V.; Vesztergombi, G.; Zsigmond, A. J.; Beni, N.; Czellar, S.; Karancsi, J.; Molnar, J.; Palinkas, J.; Szillasi, Z.; Raics, P.; Trocsanyi, Z. L.; Ujvari, B.; Swain, S. K.; Beri, S. B.; Bhatnagar, V.; Dhingra, N.; Gupta, R.; Bhawandeep, U.; Kalsi, A. K.; Kaur, M.; Mittal, M.; Nishu, N.; Singh, J. B.; Kumar, Ashok; Kumar, Arun; Ahuja, S.; Bhardwaj, A.; Choudhary, B. C.; Kumar, A.; Malhotra, S.; Naimuddin, M.; Ranjan, K.; Sharma, V.; Banerjee, S.; Bhattacharya, S.; Chatterjee, K.; Dutta, S.; Gomber, B.; Jain, Sa.; Jain, Sh.; Khurana, R.; Modak, A.; Mukherjee, S.; Roy, D.; Sarkar, S.; Sharan, M.; Abdulsalam, A.; Dutta, D.; Kailas, S.; Kumar, V.; Mohanty, A. K.; Pant, L. M.; Shukla, P.; Topkar, A.; Aziz, T.; Banerjee, S.; Bhowmik, S.; Chatterjee, R. M.; Dewanjee, R. K.; Dugad, S.; Ganguly, S.; Ghosh, S.; Guchait, M.; Gurtu, A.; Kole, G.; Kumar, S.; Maity, M.; Majumder, G.; Mazumdar, K.; Mohanty, G. B.; Parida, B.; Sudhakar, K.; Wickramage, N.; Bakhshiansohi, H.; Behnamian, H.; Etesami, S. M.; Fahim, A.; Goldouzian, R.; Jafari, A.; Khakzad, M.; Mohammadi Najafabadi, M.; Naseri, M.; Paktinat Mehdiabadi, S.; Safarzadeh, B.; Zeinali, M.; Felcini, M.; Grunewald, M.; Abbrescia, M.; Barbone, L.; Calabria, C.; Chhibra, S. S.; Colaleo, A.; Creanza, D.; De Filippis, N.; De Palma, M.; Fiore, L.; Iaselli, G.; Maggi, G.; Maggi, M.; My, S.; Nuzzo, S.; Pompili, A.; Pugliese, G.; Radogna, R.; Selvaggi, G.; Silvestris, L.; Singh, G.; Venditti, R.; Verwilligen, P.; Zito, G.; Abbiendi, G.; Benvenuti, A. C.; Bonacorsi, D.; Braibant-Giacomelli, S.; Brigliadori, L.; Campanini, R.; Capiluppi, P.; Castro, A.; Cavallo, F. R.; Codispoti, G.; Cuffiani, M.; Dallavalle, G. M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Grandi, C.; Guiducci, L.; Marcellini, S.; Masetti, G.; Montanari, A.; Navarria, F. L.; Perrotta, A.; Primavera, F.; Rossi, A. M.; Rovelli, T.; Siroli, G. P.; Tosi, N.; Travaglini, R.; Albergo, S.; Cappello, G.; Chiorboli, M.; Costa, S.; Giordano, F.; Potenza, R.; Tricomi, A.; Tuve, C.; Barbagli, G.; Ciulli, V.; Civinini, C.; D'Alessandro, R.; Focardi, E.; Gallo, E.; Gonzi, S.; Gori, V.; Lenzi, P.; Meschini, M.; Paoletti, S.; Sguazzoni, G.; Tropiano, A.; Benussi, L.; Bianco, S.; Fabbri, F.; Piccolo, D.; Ferro, F.; Lo Vetere, M.; Robutti, E.; Tosi, S.; Dinardo, M. E.; Dini, P.; Fiorendi, S.; Gennai, S.; Gerosa, R.; Ghezzi, A.; Govoni, P.; Lucchini, M. T.; Malvezzi, S.; Manzoni, R. A.; Martelli, A.; Marzocchi, B.; Menasce, D.; Moroni, L.; Paganoni, M.; Ragazzi, S.; Redaelli, N.; Tabarelli de Fatis, T.; Buontempo, S.; Cavallo, N.; Di Guida, S.; Fabozzi, F.; Iorio, A. O. M.; Lista, L.; Meola, S.; Merola, M.; Paolucci, P.; Azzi, P.; Bacchetta, N.; Bisello, D.; Branca, A.; Carlin, R.; Checchia, P.; Dall'Osso, M.; Dorigo, T.; Galanti, M.; Gasparini, F.; Gasparini, U.; Giubilato, P.; Gonella, F.; Gozzelino, A.; Kanishchev, K.; Lacaprara, S.; Margoni, M.; Meneguzzo, A. T.; Montecassiano, F.; Pazzini, J.; Pozzobon, N.; Ronchese, P.; Simonetto, F.; Torassa, E.; Tosi, M.; Zotto, P.; Zucchetta, A.; Gabusi, M.; Ratti, S. P.; Riccardi, C.; Salvini, P.; Vitulo, P.; Biasini, M.; Bilei, G. M.; Ciangottini, D.; Fanò, L.; Lariccia, P.; Mantovani, G.; Menichelli, M.; Romeo, F.; Saha, A.; Santocchia, A.; Spiezia, A.; Androsov, K.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Broccolo, G.; Castaldi, R.; Ciocci, M. A.; Dell'Orso, R.; Donato, S.; Fiori, F.; Foà, L.; Giassi, A.; Grippo, M. T.; Ligabue, F.; Lomtadze, T.; Martini, L.; Messineo, A.; Moon, C. S.; Palla, F.; Rizzi, A.; Savoy-Navarro, A.; Serban, A. T.; Spagnolo, P.; Squillacioti, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Vernieri, C.; Barone, L.; Cavallari, F.; Del Re, D.; Diemoz, M.; Grassi, M.; Jorda, C.; Longo, E.; Margaroli, F.; Meridiani, P.; Micheli, F.; Nourbakhsh, S.; Organtini, G.; Paramatti, R.; Rahatlou, S.; Rovelli, C.; Santanastasio, F.; Soffi, L.; Traczyk, P.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Bellan, R.; Biino, C.; Cartiglia, N.; Casasso, S.; Costa, M.; Degano, A.; Demaria, N.; Finco, L.; Mariotti, C.; Maselli, S.; Migliore, E.; Monaco, V.; Musich, M.; Obertino, M. M.; Ortona, G.; Pacher, L.; Pastrone, N.; Pelliccioni, M.; Pinna Angioni, G. L.; Potenza, A.; Romero, A.; Ruspa, M.; Sacchi, R.; Solano, A.; Staiano, A.; Tamponi, U.; Belforte, S.; Candelise, V.; Casarsa, M.; Cossutti, F.; Della Ricca, G.; Gobbo, B.; La Licata, C.; Marone, M.; Montanino, D.; Schizzi, A.; Umer, T.; Zanetti, A.; Kim, T. J.; Chang, S.; Kropivnitskaya, A.; Nam, S. K.; Kim, D. H.; Kim, G. N.; Kim, M. 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W.; Driga, O.; Elmer, P.; Hebda, P.; Hunt, A.; Koay, S. A.; Lujan, P.; Marlow, D.; Medvedeva, T.; Mooney, M.; Olsen, J.; Piroué, P.; Quan, X.; Saka, H.; Stickland, D.; Tully, C.; Werner, J. S.; Zenz, S. C.; Zuranski, A.; Brownson, E.; Mendez, H.; Ramirez Vargas, J. E.; Alagoz, E.; Barnes, V. E.; Benedetti, D.; Bolla, G.; Bortoletto, D.; De Mattia, M.; Hu, Z.; Jha, M. K.; Jones, M.; Jung, K.; Kress, M.; Leonardo, N.; Lopes Pegna, D.; Maroussov, V.; Merkel, P.; Miller, D. H.; Neumeister, N.; Radburn-Smith, B. C.; Shi, X.; Shipsey, I.; Silvers, D.; Svyatkovskiy, A.; Wang, F.; Xie, W.; Xu, L.; Yoo, H. D.; Zablocki, J.; Zheng, Y.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Ecklund, K. M.; Geurts, F. J. M.; Li, W.; Michlin, B.; Padley, B. P.; Redjimi, R.; Roberts, J.; Zabel, J.; Betchart, B.; Bodek, A.; Covarelli, R.; de Barbaro, P.; Demina, R.; Eshaq, Y.; Ferbel, T.; Garcia-Bellido, A.; Goldenzweig, P.; Han, J.; Harel, A.; Khukhunaishvili, A.; Petrillo, G.; Vishnevskiy, D.; Ciesielski, R.; Demortier, L.; Goulianos, K.; Lungu, G.; Mesropian, C.; Arora, S.; Barker, A.; Chou, J. P.; Contreras-Campana, C.; Contreras-Campana, E.; Duggan, D.; Ferencek, D.; Gershtein, Y.; Gray, R.; Halkiadakis, E.; Hidas, D.; Lath, A.; Panwalkar, S.; Park, M.; Patel, R.; Salur, S.; Schnetzer, S.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Rose, K.; Spanier, S.; York, A.; Bouhali, O.; Eusebi, R.; Flanagan, W.; Gilmore, J.; Kamon, T.; Khotilovich, V.; Krutelyov, V.; Montalvo, R.; Osipenkov, I.; Pakhotin, Y.; Perloff, A.; Roe, J.; Rose, A.; Safonov, A.; Sakuma, T.; Suarez, I.; Tatarinov, A.; Akchurin, N.; Cowden, C.; Damgov, J.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Kovitanggoon, K.; Kunori, S.; Lee, S. W.; Libeiro, T.; Volobouev, I.; Appelt, E.; Delannoy, A. G.; Greene, S.; Gurrola, A.; Johns, W.; Maguire, C.; Mao, Y.; Melo, A.; Sharma, M.; Sheldon, P.; Snook, B.; Tuo, S.; Velkovska, J.; Arenton, M. W.; Boutle, S.; Cox, B.; Francis, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Lin, C.; Neu, C.; Wood, J.; Harr, R.; Karchin, P. E.; Kottachchi Kankanamge Don, C.; Lamichhane, P.; Sturdy, J.; Belknap, D. A.; Carlsmith, D.; Cepeda, M.; Dasu, S.; Duric, S.; Friis, E.; Hall-Wilton, R.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Lazaridis, C.; Levine, A.; Loveless, R.; Mohapatra, A.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ross, I.; Sarangi, T.; Savin, A.; Smith, W. H.; Woods, N.

2014-11-01

A search for heavy, right-handed neutrinos, (), and right-handed bosons, which arise in the left-right symmetric extensions of the standard model, has been performed by the CMS experiment. The search was based on a sample of two lepton plus two jet events collected in proton-proton collisions at a center-of-mass energy of 8 corresponding to an integrated luminosity of 19.7 . For models with strict left-right symmetry, and assuming only one flavor contributes significantly to the decay width, the region in the two-dimensional mass plane excluded at a 95 % confidence level extends to approximately and covers a large range of neutrino masses below the boson mass, depending on the value of . This search significantly extends the exclusion region beyond previous results.

Development of a One-Stop Data Search and Discovery Engine using Ontologies for Semantic Mappings (HydroSeek)

NASA Astrophysics Data System (ADS)

Piasecki, M.; Beran, B.

2007-12-01

Search engines have changed the way we see the Internet. The ability to find the information by just typing in keywords was a big contribution to the overall web experience. While the conventional search engine methodology worked well for textual documents, locating scientific data remains a problem since they are stored in databases not readily accessible by search engine bots. Considering different temporal, spatial and thematic coverage of different databases, especially for interdisciplinary research it is typically necessary to work with multiple data sources. These sources can be federal agencies which generally offer national coverage or regional sources which cover a smaller area with higher detail. However for a given geographic area of interest there often exists more than one database with relevant data. Thus being able to query multiple databases simultaneously is a desirable feature that would be tremendously useful for scientists. Development of such a search engine requires dealing with various heterogeneity issues. In scientific databases, systems often impose controlled vocabularies which ensure that they are generally homogeneous within themselves but are semantically heterogeneous when moving between different databases. This defines the boundaries of possible semantic related problems making it easier to solve than with the conventional search engines that deal with free text. We have developed a search engine that enables querying multiple data sources simultaneously and returns data in a standardized output despite the aforementioned heterogeneity issues between the underlying systems. This application relies mainly on metadata catalogs or indexing databases, ontologies and webservices with virtual globe and AJAX technologies for the graphical user interface. Users can trigger a search of dozens of different parameters over hundreds of thousands of stations from multiple agencies by providing a keyword, a spatial extent, i.e. a bounding box, and a temporal bracket. As part of this development we have also added an environment that allows users to do some of the semantic tagging, i.e. the linkage of a variable name (which can be anything they desire) to defined concepts in the ontology structure which in turn provides the backbone of the search engine.

What Searches Do Users Run on PEDro? An Analysis of 893,971 Search Commands Over a 6-Month Period.

PubMed

Stevens, Matthew L; Moseley, Anne; Elkins, Mark R; Lin, Christine C-W; Maher, Chris G

2016-08-05

Clinicians must be able to search effectively for relevant research if they are to provide evidence-based healthcare. It is therefore relevant to consider how users search databases of evidence in healthcare, including what information users look for and what search strategies they employ. To date such analyses have been restricted to the PubMed database. Although the Physiotherapy Evidence Database (PEDro) is searched millions of times each year, no studies have investigated how users search PEDro. To assess the content and quality of searches conducted on PEDro. Searches conducted on the PEDro website over 6 months were downloaded and the 'get' commands and page-views extracted. The following data were tabulated: the 25 most common searches; the number of search terms used; the frequency of use of simple and advanced searches, including the use of each advanced search field; and the frequency of use of various search strategies. Between August 2014 and January 2015, 893,971 search commands were entered on PEDro. Fewer than 18 % of these searches used the advanced search features of PEDro. 'Musculoskeletal' was the most common subdiscipline searched, while 'low back pain' was the most common individual search. Around 20 % of all searches contained errors. PEDro is a commonly used evidence resource, but searching appears to be sub-optimal in many cases. The effectiveness of searches conducted by users needs to improve, which could be facilitated by methods such as targeted training and amending the search interface.

Outdoor workers' sun-related knowledge, attitudes and protective behaviours: a systematic review of cross-sectional and interventional studies.

PubMed

Reinau, D; Weiss, M; Meier, C R; Diepgen, T L; Surber, C

2013-05-01

Sun protection is a major concern for outdoor workers as they are particularly exposed to solar ultraviolet radiation and therefore at increased risk of developing some forms of skin cancer, cataract and ocular neoplasm. In order to provide an overview of outdoor workers' sun-related knowledge, attitudes and protective behaviours as reported in the literature and to evaluate the effectiveness of sun-safety education programmes in outdoor occupational settings, we conducted a systematic review of the literature by searching three electronic databases (PubMed, Embase, PsycINFO) from their inception up to 25 April 2012. An extensive hand search complemented the database searches. We identified 34 relevant articles on descriptive studies and 18 articles on interventional studies. Considerable numbers of outdoor workers were found to have sun-sensitive skin types; sunburn rates per season ranged from 50% to 80%. Data concerning outdoor workers' sun-related knowledge and attitudes were scarce and controversial. The reported sun-protective behaviours were largely inadequate, with many workers stating that they never or only rarely wore a long-sleeved shirt (50-80%), sun-protective headgear (30-80%) and sunscreen (30-100%) while working in the sun. However, there is growing evidence that occupational sun-safety education is effective in increasing outdoor workers' sun-protection habits and presumably in decreasing sunburn rates. Occupational sun-safety education programmes offer great potential for improving outdoor workers' largely insufficient sun-protective behaviours. It is hoped that, in the future, committed support from healthcare authorities, cancer foundations, employers and dermatologists will open the way for rapid and uncomplicated implementation of sun-safety education programmes. © 2012 The Authors. BJD © 2012 British Association of Dermatologists.

Measurement tools of resource use and quality of life in clinical trials for dementia or cognitive impairment interventions: protocol for a scoping review.

PubMed

Yang, Fan; Dawes, Piers; Leroi, Iracema; Gannon, Brenda

2017-01-26

Dementia and cognitive impairment could severely impact patients' life and bring heavy burden to patients, caregivers and societies. Some interventions are suggested for the older patients with these conditions to help them live well, but economic evaluation is needed to assess the cost-effectiveness of these interventions. Trial-based economic evaluation is an ideal method; however, little is known about the tools used to collect data of resource use and quality of life alongside the trials. Therefore, the aim of this review is to identify and describe the resource use and quality of life instruments in clinical trials of interventions for older patients with dementia or cognitive impairment. We will perform a search in main electronic databases (Ovid MEDLINE, PsycINFO, EMBASE, CINAHL, Cochrane Databases of Systematic Reviews, Web of Science and Scopus) using the key terms or their synonyms: older, dementia, cognitive impairment, cost, quality of life, intervention and tools. After removing duplicates, two independent reviewers will screen each entry for eligibility, initially by title and abstract, then by full-text. A hand search of the references of included articles and general search, e.g. Google Scholar, will also be conducted to identify potential relevant studies. All disagreements will be resolved by discussion or consultation with a third reviewer if necessary. Data analysis will be completed and reported in a narrative review. This review will identify the instruments used in clinical trials to collect resource use and quality of life data for dementia or cognitive impairment interventions. This will help to guide the study design of future trial-based economic evaluation of these interventions. PROSPERO CRD42016038495.

Advantages and Challenges of Dried Blood Spot Analysis by Mass Spectrometry Across the Total Testing Process

PubMed Central

Zakaria, Rosita; Allen, Katrina J.; Koplin, Jennifer J.; Roche, Peter

2016-01-01

Introduction Through the introduction of advanced analytical techniques and improved throughput, the scope of dried blood spot testing utilising mass spectrometric methods, has broadly expanded. Clinicians and researchers have become very enthusiastic about the potential applications of dried blood spot based mass spectrometric applications. Analysts on the other hand face challenges of sensitivity, reproducibility and overall accuracy of dried blood spot quantification. In this review, we aim to bring together these two facets to discuss the advantages and current challenges of non-newborn screening applications of dried blood spot quantification by mass spectrometry. Methods To address these aims we performed a key word search of the PubMed and MEDLINE online databases in conjunction with individual manual searches to gather information. Keywords for the initial search included; “blood spot” and “mass spectrometry”; while excluding “newborn”; and “neonate”. In addition, databases were restricted to English language and human specific. There was no time period limit applied. Results As a result of these selection criteria, 194 references were identified for review. For presentation, this information is divided into: 1) clinical applications; and 2) analytical considerations across the total testing process; being pre-analytical, analytical and post-analytical considerations. Conclusions DBS analysis using MS applications is now broadly applied, with drug monitoring for both therapeutic and toxicological analysis being the most extensively reported. Several parameters can affect the accuracy of DBS measurement and further bridge experiments are required to develop adjustment rules for comparability between dried blood spot measures and the equivalent serum/plasma values. Likewise, the establishment of independent reference intervals for dried blood spot sample matrix is required. PMID:28149263

Mortality and injuries among Iranians in Iraq-Iran war: a systematic review.

PubMed

Salamati, Payman; Razavi, Seyed Mansour; Shokraneh, Farhad; Mohazzab Torabi, Saman; Laal, Marjan; Hadjati, Gholamreza; Khaji, Ali; Rahimi Movaghar, Vafa

2013-09-01

The Iraq-Iran war was one of the longest conflicts in the twentieth century. The aim of our research was to review the incidence of mortality and injuries of the war. A search strategy was designed and run in Medline, EMBASE, Scopus, and Iranian databases including Scientific Information Database (SID), IranMedex, and Magiran. Also, searching grey literature, checking references, tracking citations, hand-searching of focused journals, and websites were utilized for retrieval of related studies. All of articles which studied epidemiology of mortality or injuries of the war were included. The excluding criteria were case reports, case series, laboratory researches, and nonoriginal studies. Fourteen articles out of 1751 primary results were selected to be included in the study. During the war (1980 - 1988), 188,015 to 217,489 Iranians were killed (about 70 people per day). The mean age of mortality was 23 years. Six thousand four hundred twenty-seven (2.9%) of those who died during the war were females. One thousand five chemical warfare victims died between 1983 and 1994. From 1985 through 1998, 82 veterans had successful suicides too. At the end of war, we had 398, 587 veterans who needed follow- up. Among them, there were 52,000 chemical warfare victims. Between 1988 and 2003, 1400 people died and 2313 injured due to landmines and unexploded ordnances in five border provinces. The war caused a lot of mortalities and morbidities in our country. Now, 24 years after the war, many physically, mentally, and chemically injured victims have remained. We suggest other studies about indirect impacts of the war on societies, families, friends, and affiliates of the victims.

Pain perception during levonorgestrel-releasing intrauterine device insertion in nulliparous women: a systematic review.

PubMed

Anthoulakis, Christos; Iordanidou, Eirini; Vatopolou, Anastasia

2018-06-08

Intrauterine devices (IUDs) still remain underused in adolescents. Pain during insertion may prevent adolescents to opt for a levonorgestrel (LNG) - releasing IUD. This study aimed to conduct a systematic review, following the PRISMA guidelines, and critically appraise published data with respect to the efficacy of various substances (analgesics or not) in preventing pain during LNG-IUD insertion in nulliparous women as a proxy for adolescents. DESIGN, SETTING, PARTICIPANTS, INTERVENTIONS, AND MAIN OUTCOME MEASURES: A comprehensive computerized systematic literature search of all English language studies between 2006 and 2016 was performed in PubMed, EMBASE, Scopus, Evidence Based Medicine Reviews (Cochrane Database and Cochrane Central Register of Controlled Trials), and Google Scholar. Relevant article reference lists were hand searched. Computerised database search revealed 31 citations of relevance, 9 of which with a total of 355 treated women and 345 controls fulfilled the inclusion/exclusion criteria. In women treated with misoprostol (n=150) versus placebo (n=145), the median visual analog scale (VAS) score ± standard deviation (SD) were 5.7 ± 2.1 versus 5.1 ± 2.2, respectively. In the abovementioned population, there was a non-significant change in VAS score (OR=1.44, 95%CI 0.86-2.40). In women treated with lidocaine (n=140) versus placebo (n=136), the median VAS score ± SD were 4.6 ± 2.1 versus 5.8 ± 2, respectively. In the aforementioned population, there was a significant decrease in VAS score (OR=0.12, 95%CI 0.02-0.91). In nulliparous women, lidocaine treatment seems to be a reasonable choice. However, further studies are required to examine the different routes and modes of administration as well as optimal quantities. Copyright © 2018. Published by Elsevier Inc.

Repair of restorations--criteria for decision making and clinical recommendations.

PubMed

Hickel, Reinhard; Brüshaver, Katrin; Ilie, Nicoleta

2013-01-01

In the last decade, repair of restorations has become more and more popular while teaching repair of restorations is now included in most universities in Europe and North America. The aim of this paper was therefore to systematically review the clinical and the in vitro aspects of repair of restorations by considering different restorative materials--resin-based composites, amalgam, glass-ionomer cements, ceramics or metals. The paper gives also an overview of the occurrences of teaching repair in different universities. Furthermore, the paper outlines criteria for decision making when to treat a defect restoration with refurbishment, repair, replacement or no treatment. The database search strategy for resin based composite restoration repair (n=360) and the following hand search (n=95) retrieved 455 potentially eligible studies. After de-duplication, 260 records were examined by the titles and abstracts. 154 studies were excluded and 106 articles were assessed for eligibility by analyzing the full texts. Following the same search and selection process, 42 studies for amalgam repair, 51 studies for cast, inlay or porcelain restoration repair and 8 studies for teaching were assessed for eligibility by analysis of the full texts. Following databases were analyzed: Cochrane Library, MEDLINE, EMBASE, BIOSIS and PUBMED. Papers were selected if they met the following criteria: replacement, refurbishment or repair of resin composite restorations or amalgam restorations or inlay, cast restoration or porcelain repair. Clinical studies, in vitro studies and reports about teaching were included. Repair of restoration is a valuable method to improve the quality of restorations and is accepted, practiced and taught in many universities. However, there is a need for methodologically sound randomized controlled long-term clinical trials to be able to give an evidence based recommendation. Copyright © 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Clinical review: Brain-body temperature differences in adults with severe traumatic brain injury

PubMed Central

2013-01-01

Surrogate or 'proxy' measures of brain temperature are used in the routine management of patients with brain damage. The prevailing view is that the brain is 'hotter' than the body. The polarity and magnitude of temperature differences between brain and body, however, remains unclear after severe traumatic brain injury (TBI). The focus of this systematic review is on the adult patient admitted to intensive/neurocritical care with a diagnosis of severe TBI (Glasgow Coma Scale score of less than 8). The review considered studies that measured brain temperature and core body temperature. Articles published in English from the years 1980 to 2012 were searched in databases, CINAHL, PubMed, Scopus, Web of Science, Science Direct, Ovid SP, Mednar and ProQuest Dissertations & Theses Database. For the review, publications of randomised controlled trials, non-randomised controlled trials, before and after studies, cohort studies, case-control studies and descriptive studies were considered for inclusion. Of 2,391 records identified via the search strategies, 37 were retrieved for detailed examination (including two via hand searching). Fifteen were reviewed and assessed for methodological quality. Eleven studies were included in the systematic review providing 15 brain-core body temperature comparisons. The direction of mean brain-body temperature differences was positive (brain higher than body temperature) and negative (brain lower than body temperature). Hypothermia is associated with large brain-body temperature differences. Brain temperature cannot be predicted reliably from core body temperature. Concurrent monitoring of brain and body temperature is recommended in patients where risk of temperature-related neuronal damage is a cause for clinical concern and when deliberate induction of below-normal body temperature is instituted. PMID:23680353

Scientists Admitting to Plagiarism: A Meta-analysis of Surveys.

PubMed

Pupovac, Vanja; Fanelli, Daniele

2015-10-01

We conducted a systematic review and meta-analysis of anonymous surveys asking scientists whether they ever committed various forms of plagiarism. From May to December 2011 we searched 35 bibliographic databases, five grey literature databases and hand searched nine journals for potentially relevant studies. We included surveys that asked scientists if, in a given recall period, they had committed or knew of a colleague who committed plagiarism, and from each survey extracted the proportion of those who reported at least one case. Studies that focused on academic (i.e. student) plagiarism were excluded. Literature searches returned 12,460 titles from which 17 relevant survey studies were identified. Meta-analysis of studies reporting committed (N = 7) and witnessed (N = 11) plagiarism yielded a pooled estimate of, respectively, 1.7% (95% CI 1.2-2.4) and 30% (95% CI 17-46). Basic methodological factors, including sample size, year of survey, delivery method and whether survey questions were explicit rather than indirect made a significant difference on survey results. Even after controlling for these methodological factors, between-study differences in admission rates were significantly above those expected by sampling error alone and remained largely unexplained. Despite several limitations of the data and of this meta-analysis, we draw three robust conclusions: (1) The rate at which scientists report knowing a colleague who committed plagiarism is higher than for data fabrication and falsification; (2) The rate at which scientists report knowing a colleague who committed plagiarism is correlated to that of fabrication and falsification; (3) The rate at which scientists admit having committed either form of misconduct (i.e. fabrication, falsification and plagiarism) in surveys has declined over time.

Building the capacity of policy-makers and planners to strengthen mental health systems in low- and middle-income countries: a systematic review.

PubMed

Keynejad, Roxanne; Semrau, Maya; Toynbee, Mark; Evans-Lacko, Sara; Lund, Crick; Gureje, Oye; Ndyanabangi, Sheila; Courtin, Emilie; Abdulmalik, Jibril O; Alem, Atalay; Fekadu, Abebaw; Thornicroft, Graham; Hanlon, Charlotte

2016-10-21

Little is known about the interventions required to build the capacity of mental health policy-makers and planners in low- and middle-income countries (LMICs). We conducted a systematic review with the primary aim of identifying and synthesizing the evidence base for building the capacity of policy-makers and planners to strengthen mental health systems in LMICs. We searched MEDLINE, Embase, PsycINFO, Web of Knowledge, Web of Science, Scopus, CINAHL, LILACS, ScieELO, Google Scholar and Cochrane databases for studies reporting evidence, experience or evaluation of capacity-building of policy-makers, service planners or managers in mental health system strengthening in LMICs. Reports in English, Spanish, Portuguese, French or German were included. Additional papers were identified by hand-searching references and contacting experts and key informants. Database searches yielded 2922 abstracts and 28 additional papers were identified. Following screening, 409 full papers were reviewed, of which 14 fulfilled inclusion criteria for the review. Data were extracted from all included papers and synthesized into a narrative review. Only a small number of mental health system-related capacity-building interventions for policy-makers and planners in LMICs were described. Most models of capacity-building combined brief training with longer term mentorship, dialogue and/or the establishment of networks of support. However, rigorous research and evaluation methods were largely absent, with studies being of low quality, limiting the potential to separate mental health system strengthening outcomes from the effects of associated contextual factors. This review demonstrates the need for partnership approaches to building the capacity of mental health policy-makers and planners in LMICs, assessed rigorously against pre-specified conceptual frameworks and hypotheses, utilising longitudinal evaluation and mixed quantitative and qualitative approaches.

The Giardia genome project database.

PubMed

McArthur, A G; Morrison, H G; Nixon, J E; Passamaneck, N Q; Kim, U; Hinkle, G; Crocker, M K; Holder, M E; Farr, R; Reich, C I; Olsen, G E; Aley, S B; Adam, R D; Gillin, F D; Sogin, M L

2000-08-15

The Giardia genome project database provides an online resource for Giardia lamblia (WB strain, clone C6) genome sequence information. The database includes edited single-pass reads, the results of BLASTX searches, and details of progress towards sequencing the entire 12 million-bp Giardia genome. Pre-sorted BLASTX results can be retrieved based on keyword searches and BLAST searches of the high throughput Giardia data can be initiated from the web site or through NCBI. Descriptions of the genomic DNA libraries, project protocols and summary statistics are also available. Although the Giardia genome project is ongoing, new sequences are made available on a bi-monthly basis to ensure that researchers have access to information that may assist them in the search for genes and their biological function. The current URL of the Giardia genome project database is www.mbl.edu/Giardia.

Multimedia explorer: image database, image proxy-server and search-engine.

PubMed Central

Frankewitsch, T.; Prokosch, U.

1999-01-01

Multimedia plays a major role in medicine. Databases containing images, movies or other types of multimedia objects are increasing in number, especially on the WWW. However, no good retrieval mechanism or search engine currently exists to efficiently track down such multimedia sources in the vast of information provided by the WWW. Secondly, the tools for searching databases are usually not adapted to the properties of images. HTML pages do not allow complex searches. Therefore establishing a more comfortable retrieval involves the use of a higher programming level like JAVA. With this platform independent language it is possible to create extensions to commonly used web browsers. These applets offer a graphical user interface for high level navigation. We implemented a database using JAVA objects as the primary storage container which are then stored by a JAVA controlled ORACLE8 database. Navigation depends on a structured vocabulary enhanced by a semantic network. With this approach multimedia objects can be encapsulated within a logical module for quick data retrieval. PMID:10566463

Multimedia explorer: image database, image proxy-server and search-engine.

PubMed

Frankewitsch, T; Prokosch, U

1999-01-01

Multimedia plays a major role in medicine. Databases containing images, movies or other types of multimedia objects are increasing in number, especially on the WWW. However, no good retrieval mechanism or search engine currently exists to efficiently track down such multimedia sources in the vast of information provided by the WWW. Secondly, the tools for searching databases are usually not adapted to the properties of images. HTML pages do not allow complex searches. Therefore establishing a more comfortable retrieval involves the use of a higher programming level like JAVA. With this platform independent language it is possible to create extensions to commonly used web browsers. These applets offer a graphical user interface for high level navigation. We implemented a database using JAVA objects as the primary storage container which are then stored by a JAVA controlled ORACLE8 database. Navigation depends on a structured vocabulary enhanced by a semantic network. With this approach multimedia objects can be encapsulated within a logical module for quick data retrieval.

Ethical guidelines, animal profile, various animal models used in periodontal research with alternatives and future perspectives.

PubMed

Pasupuleti, Mohan Kumar; Molahally, Subramanya Shetty; Salwaji, Supraja

2016-01-01

Laboratory animal models serve as a facilitator to investigate the etiopathogenesis of periodontal disease, are used to know the efficacy of reconstructive and regenerative procedures, and are also helpful in evaluation of newer therapeutic techniques including laser and implant therapies prior to application in the human beings. The aim of this review is to know the different animal models used in various specialties of dental research and to know the ethical guidelines prior to the usage of experimental models with main emphasis on how to refine, replace, and reduce the number of animal models usage in the laboratory. An online search for experimental animal models used in dental research was performed using MEDLINE/PubMed database. Publications from 2009 to May 2013 in the specialty of periodontics were included in writing this review. A total of 652 references were published in PubMed/MEDLINE databases based on the search terms used. Out of 245 studies, 241 were related to the periodontal research published in English from 2009 to 2013. Relevant papers were chosen according to the inclusion and exclusion criteria. After extensive electronic and hand search on animal models, it has been observed that various animal models were used in dental research. Search on animal models used for dental research purpose revealed that various animals such as rats, mice, guinea pigs, rabbit, beagle dogs, goats, and nonhuman primates were extensively used. However, with the new advancement of ex vivo animal models, it has become easy to investigate disease pathogenesis and to test the efficacy of newer therapeutic modalities with the reduced usage of animal models. This review summarized the large amount of literature on animal models used in periodontal research with main emphasis on ethical guidelines and on reducing the animal model usage in future perspective.

Cultural aspects of adjustment to coronary heart disease in Chinese-Australians: a review of the literature.

PubMed

Daly, John; Davidson, Patricia; Chang, Esther; Hancock, Karen; Rees, David; Thompson, David R

2002-08-01

The burden of illness associated with Coronary Heart Disease (CHD) has determined this as a key focus for research at a basic science, individual and population level. Although considerable research has been conducted on specific aspects of the experience of CHD, such as anxiety or depression, there is a lack of research investigating the global aspects of the illness experience from the individual's perspective. Furthermore, there is a paucity of research examining the cross-cultural experiences of patients from Non-English Speaking Backgrounds (NESB). Given the multicultural nature of Australian society, and that health and illness are culturally constructed experiences (Manderson 1990), it is important to include the perspectives of people from minority cultures in health related research in order to provide culturally sensitive and appropriate health care and information during an illness. Further, the potential to prevent and modulate the course of CHD, by strategies such as smoking cessation and lipid management, mandate a health promotion agenda based on equity and access for all members of society. This article discusses cultural aspects of CHD in relation to nursing and allied health care during the recovery phase of an acute cardiac event. It reviews the research that has been conducted in this area, focusing on the Chinese-Australian population. The CINAHL, MEDLINE, FAMILY (Australian Family and Society Abstracts Database), PsychINFO, and Multicultural Australian and immigration Studies (MAIS) databases were searched, identifying literature published from 1982. Keywords used were Chin* (Chinese, China), Asia* (Asia, Asian), experience, adjustment, psychological, heart, coronary, cardiac, health and services. Reports not written in English were excluded. Australian Government reports were also searched, as well as hand searching of nursing and medical textbooks. These searches resulted in over 1000 articles. However, only around 50 were relevant for this review. Chinese-Australians are one of the fastest growing populations in Australia, and are at increased risk of CHD upon settling to Australia. Recommendations for future research and for the practice of nursing are provided.

Ethical guidelines, animal profile, various animal models used in periodontal research with alternatives and future perspectives

PubMed Central

Pasupuleti, Mohan Kumar; Molahally, Subramanya Shetty; Salwaji, Supraja

2016-01-01

Laboratory animal models serve as a facilitator to investigate the etiopathogenesis of periodontal disease, are used to know the efficacy of reconstructive and regenerative procedures, and are also helpful in evaluation of newer therapeutic techniques including laser and implant therapies prior to application in the human beings. The aim of this review is to know the different animal models used in various specialties of dental research and to know the ethical guidelines prior to the usage of experimental models with main emphasis on how to refine, replace, and reduce the number of animal models usage in the laboratory. An online search for experimental animal models used in dental research was performed using MEDLINE/PubMed database. Publications from 2009 to May 2013 in the specialty of periodontics were included in writing this review. A total of 652 references were published in PubMed/MEDLINE databases based on the search terms used. Out of 245 studies, 241 were related to the periodontal research published in English from 2009 to 2013. Relevant papers were chosen according to the inclusion and exclusion criteria. After extensive electronic and hand search on animal models, it has been observed that various animal models were used in dental research. Search on animal models used for dental research purpose revealed that various animals such as rats, mice, guinea pigs, rabbit, beagle dogs, goats, and nonhuman primates were extensively used. However, with the new advancement of ex vivo animal models, it has become easy to investigate disease pathogenesis and to test the efficacy of newer therapeutic modalities with the reduced usage of animal models. This review summarized the large amount of literature on animal models used in periodontal research with main emphasis on ethical guidelines and on reducing the animal model usage in future perspective. PMID:28298815

An evidence based review of the assessment and management of penetrating neck trauma.

PubMed

Burgess, C A; Dale, O T; Almeyda, R; Corbridge, R J

2012-02-01

Although relatively uncommon, penetrating neck trauma has the potential for serious morbidity and an estimated mortality of up to 6%. The assessment and management of patients who have sustained a penetrating neck injury has historically been an issue surrounded by significant controversy. OBJECTIVES OF REVIEW: To assess recent evidence relating to the assessment and management of penetrating neck trauma, highlighting areas of controversy with an overall aim of formulating clinical guidelines according to a care pathway format. Structured, non-systematic review of recent medical literature. An electronic literature search was performed in May 2011. The Medline database was searched using the Medical Subject Headings terms 'neck injuries' and 'wounds, penetrating' in conjunction with the terms 'assessment' or 'management'. Embase was searched with the terms 'penetrating trauma' and 'neck injury', also in conjunction with the terms 'assessment' and 'management'. Results were limited to articles published in English from 1990 to the present day. Abstracts were reviewed by the first three authors to select full-text articles for further critical appraisal. The references and citation links of these articles were hand-searched to identify further articles of relevance. 147 relevant articles were identified by the electronic literature search, comprising case series, case reports and reviews. 33 were initially selected for further evaluation. Although controversy continues to surround the management of penetrating neck trauma, the role of selective non-operative management and the utility of CT angiography to investigate potential vascular injuries appears to be increasingly accepted. © 2011 Blackwell Publishing Ltd.

Behavioural and Developmental Interventions for Autism Spectrum Disorder: A Clinical Systematic Review

PubMed Central

Ospina, Maria B.; Krebs Seida, Jennifer; Clark, Brenda; Karkhaneh, Mohammad; Hartling, Lisa; Tjosvold, Lisa; Vandermeer, Ben; Smith, Veronica

2008-01-01

Background Much controversy exists regarding the clinical efficacy of behavioural and developmental interventions for improving the core symptoms of autism spectrum disorders (ASD). We conducted a systematic review to summarize the evidence on the effectiveness of behavioural and developmental interventions for ASD. Methods and Findings Comprehensive searches were conducted in 22 electronic databases through May 2007. Further information was obtained through hand searching journals, searching reference lists, databases of theses and dissertations, and contacting experts in the field. Experimental and observational analytic studies were included if they were written in English and reported the efficacy of any behavioural or developmental intervention for individuals with ASD. Two independent reviewers made the final study selection, extracted data, and reached consensus on study quality. Results were summarized descriptively and, where possible, meta-analyses of the study results were conducted. One-hundred-and-one studies at predominantly high risk of bias that reported inconsistent results across various interventions were included in the review. Meta-analyses of three controlled clinical trials showed that Lovaas treatment was superior to special education on measures of adaptive behaviour, communication and interaction, comprehensive language, daily living skills, expressive language, overall intellectual functioning and socialization. High-intensity Lovaas was superior to low-intensity Lovaas on measures of intellectual functioning in two retrospective cohort studies. Pooling the results of two randomized controlled trials favoured developmental approaches based on initiative interaction compared to contingency interaction in the amount of time spent in stereotyped behaviours and distal social behaviour, but the effect sizes were not clinically significant. No statistically significant differences were found for: Lovaas versus special education for non-verbal intellectual functioning; Lovaas versus Developmental Individual-difference relationship-based intervention for communication skills; computer assisted instruction versus no treatment for facial expression recognition; and TEACCH versus standard care for imitation skills and eye-hand integration. Conclusions While this review suggests that Lovaas may improve some core symptoms of ASD compared to special education, these findings are based on pooling of a few, methodologically weak studies with few participants and relatively short-term follow-up. As no definitive behavioural or developmental intervention improves all symptoms for all individuals with ASD, it is recommended that clinical management be guided by individual needs and availability of resources. PMID:19015734

MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for 
the Construction of Sequence Data Warehouses.

PubMed

Gacesa, Ranko; Zucko, Jurica; Petursdottir, Solveig K; Gudmundsdottir, Elisabet Eik; Fridjonsson, Olafur H; Diminic, Janko; Long, Paul F; Cullum, John; Hranueli, Daslav; Hreggvidsson, Gudmundur O; Starcevic, Antonio

2017-06-01

The MEGGASENSE platform constructs relational databases of DNA or protein sequences. The default functional analysis uses 14 106 hidden Markov model (HMM) profiles based on sequences in the KEGG database. The Solr search engine allows sophisticated queries and a BLAST search function is also incorporated. These standard capabilities were used to generate the SCATT database from the predicted proteome of Streptomyces cattleya . The implementation of a specialised metagenome database (AMYLOMICS) for bioprospecting of carbohydrate-modifying enzymes is described. In addition to standard assembly of reads, a novel 'functional' assembly was developed, in which screening of reads with the HMM profiles occurs before the assembly. The AMYLOMICS database incorporates additional HMM profiles for carbohydrate-modifying enzymes and it is illustrated how the combination of HMM and BLAST analyses helps identify interesting genes. A variety of different proteome and metagenome databases have been generated by MEGGASENSE.

Developing and refining the methods for a 'one-stop shop' for research evidence about health systems.

PubMed

Lavis, John N; Wilson, Michael G; Moat, Kaelan A; Hammill, Amanda C; Boyko, Jennifer A; Grimshaw, Jeremy M; Flottorp, Signe

2015-02-25

Policymakers, stakeholders and researchers have not been able to find research evidence about health systems using an easily understood taxonomy of topics, know when they have conducted a comprehensive search of the many types of research evidence relevant to them, or rapidly identify decision-relevant information in their search results. To address these gaps, we developed an approach to building a 'one-stop shop' for research evidence about health systems. We developed a taxonomy of health system topics and iteratively refined it by drawing on existing categorization schemes and by using it to categorize progressively larger bundles of research evidence. We identified systematic reviews, systematic review protocols, and review-derived products through searches of Medline, hand searches of several databases indexing systematic reviews, hand searches of journals, and continuous scanning of listservs and websites. We developed an approach to providing 'added value' to existing content (e.g., coding systematic reviews according to the countries in which included studies were conducted) and to expanding the types of evidence eligible for inclusion (e.g., economic evaluations and health system descriptions). Lastly, we developed an approach to continuously updating the online one-stop shop in seven supported languages. The taxonomy is organized by governance, financial, and delivery arrangements and by implementation strategies. The 'one-stop shop', called Health Systems Evidence, contains a comprehensive inventory of evidence briefs, overviews of systematic reviews, systematic reviews, systematic review protocols, registered systematic review titles, economic evaluations and costing studies, health reform descriptions and health system descriptions, and many types of added-value coding. It is continuously updated and new content is regularly translated into Arabic, Chinese, English, French, Portuguese, Russian, and Spanish. Policymakers and stakeholders can now easily access and use a wide variety of types of research evidence about health systems to inform decision-making and advocacy. Researchers and research funding agencies can use Health Systems Evidence to identify gaps in the current stock of research evidence and domains that could benefit from primary research, systematic reviews, and review overviews.

Characterizing the genetic structure of a forensic DNA database using a latent variable approach.

PubMed

Kruijver, Maarten

2016-07-01

Several problems in forensic genetics require a representative model of a forensic DNA database. Obtaining an accurate representation of the offender database can be difficult, since databases typically contain groups of persons with unregistered ethnic origins in unknown proportions. We propose to estimate the allele frequencies of the subpopulations comprising the offender database and their proportions from the database itself using a latent variable approach. We present a model for which parameters can be estimated using the expectation maximization (EM) algorithm. This approach does not rely on relatively small and possibly unrepresentative population surveys, but is driven by the actual genetic composition of the database only. We fit the model to a snapshot of the Dutch offender database (2014), which contains close to 180,000 profiles, and find that three subpopulations suffice to describe a large fraction of the heterogeneity in the database. We demonstrate the utility and reliability of the approach with three applications. First, we use the model to predict the number of false leads obtained in database searches. We assess how well the model predicts the number of false leads obtained in mock searches in the Dutch offender database, both for the case of familial searching for first degree relatives of a donor and searching for contributors to three-person mixtures. Second, we study the degree of partial matching between all pairs of profiles in the Dutch database and compare this to what is predicted using the latent variable approach. Third, we use the model to provide evidence to support that the Dutch practice of estimating match probabilities using the Balding-Nichols formula with a native Dutch reference database and θ=0.03 is conservative. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

SW#db: GPU-Accelerated Exact Sequence Similarity Database Search.

PubMed

Korpar, Matija; Šošić, Martin; Blažeka, Dino; Šikić, Mile

2015-01-01

In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result-the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4-5 times faster than SSEARCH, 6-25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases.

Is Library Database Searching a Language Learning Activity?

ERIC Educational Resources Information Center

Bordonaro, Karen

2010-01-01

This study explores how non-native speakers of English think of words to enter into library databases when they begin the process of searching for information in English. At issue is whether or not language learning takes place when these students use library databases. Language learning in this study refers to the use of strategies employed by…

Parallel database search and prime factorization with magnonic holographic memory devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khitun, Alexander

In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploitmore » wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.« less

Parallel database search and prime factorization with magnonic holographic memory devices

NASA Astrophysics Data System (ADS)

Khitun, Alexander

2015-12-01

In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploit wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.

Discrepancies between meeting abstracts and subsequent full text publications in hand surgery.

PubMed

Theman, Todd A; Labow, Brian I; Taghinia, Amir

2014-08-01

Research abstracts presented during the proceedings of an annual meeting are often cited and can influence clinical practice. Prior studies show that roughly 50% of abstracts at American Society for Surgery of the Hand meetings are eventually published. Yet, it is unknown how often the results or conclusions of published studies differ from the podium presentation. The objective of this study was to quantify the differences between abstracts presented during the annual meeting of the American Society for Surgery of the Hand and the resulting manuscripts. We retrospectively reviewed every abstract delivered as a podium presentation at the American Society for Surgery of the Hand annual meeting from 2000 to 2010. We searched the PubMed database for matching publications and compared authorship, country of origin, hypothesis, study design and methodology, changes in study groups or populations, results, and conclusions. Of 798 total abstracts, we analyzed 719 involving the hand, wrist, and brachial plexus. Fifty-six different journals published 393 of the abstracts, for a 49% publication rate. Mean time to publication was 18 months with a median of 14 and maximum of 122 months. There were inconsistencies between the results and/or conclusions in 14% of full-length articles compared with the abstract presented at the meeting. A total of 9% of articles were published with fewer subjects. Authorships changes were noted in 54% of publications. Abstracts represent preliminary investigations and major and minor changes occur before subsequent publication. Caution should be exercised in referencing abstracts or altering clinical practice based on their content. Economic/decision analysis IV. Copyright © 2014 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

PubMed

Deutsch, Eric W; Sun, Zhi; Campbell, David S; Binz, Pierre-Alain; Farrah, Terry; Shteynberg, David; Mendoza, Luis; Omenn, Gilbert S; Moritz, Robert L

2016-11-04

The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources from which somewhat different sequence sets can be obtained. This can lead to confusion about which database is best in which circumstances-a problem especially acute in human sample analysis. All sequence databases are genome-based, with sequences for the predicted gene and their protein translation products compiled. Our goal is to create a set of primary sequence databases that comprise the union of sequences from many of the different available sources and make the result easily available to the community. We have compiled a set of four sequence databases of varying sizes, from a small database consisting of only the ∼20,000 primary isoforms plus contaminants to a very large database that includes almost all nonredundant protein sequences from several sources. This set of tiered, increasingly complete human protein sequence databases suitable for mass spectrometry proteomics sequence database searching is called the Tiered Human Integrated Search Proteome set. In order to evaluate the utility of these databases, we have analyzed two different data sets, one from the HeLa cell line and the other from normal human liver tissue, with each of the four tiers of database complexity. The result is that approximately 0.8%, 1.1%, and 1.5% additional peptides can be identified for Tiers 2, 3, and 4, respectively, as compared with the Tier 1 database, at substantially increasing computational cost. This increase in computational cost may be worth bearing if the identification of sequence variants or the discovery of sequences that are not present in the reviewed knowledge base entries is an important goal of the study. We find that it is useful to search a data set against a simpler database, and then check the uniqueness of the discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/ .

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics

PubMed Central

Deutsch, Eric W.; Sun, Zhi; Campbell, David S.; Binz, Pierre-Alain; Farrah, Terry; Shteynberg, David; Mendoza, Luis; Omenn, Gilbert S.; Moritz, Robert L.

2016-01-01

The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources from which somewhat different sequence sets can be obtained. This can lead to confusion about which database is best in which circumstances – a problem especially acute in human sample analysis. All sequence databases are genome-based, with sequences for the predicted gene and their protein translation products compiled. Our goal is to create a set of primary sequence databases that comprise the union of sequences from many of the different available sources and make the result easily available to the community. We have compiled a set of four sequence databases of varying sizes, from a small database consisting of only the ~20,000 primary isoforms plus contaminants to a very large database that includes almost all non-redundant protein sequences from several sources. This set of tiered, increasingly complete human protein sequence databases suitable for mass spectrometry proteomics sequence database searching is called the Tiered Human Integrated Search Proteome set. In order to evaluate the utility of these databases, we have analyzed two different data sets, one from the HeLa cell line and the other from normal human liver tissue, with each of the four tiers of database complexity. The result is that approximately 0.8%, 1.1%, and 1.5% additional peptides can be identified for Tiers 2, 3, and 4, respectively, as compared with the Tier 1 database, at substantially increasing computational cost. This increase in computational cost may be worth bearing if the identification of sequence variants or the discovery of sequences that are not present in the reviewed knowledge base entries is an important goal of the study. We find that it is useful to search a data set against a simpler database, and then check the uniqueness of the discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/. PMID:27577934

STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results.

PubMed

Piehowski, Paul D; Petyuk, Vladislav A; Sandoval, John D; Burnum, Kristin E; Kiebel, Gary R; Monroe, Matthew E; Anderson, Gordon A; Camp, David G; Smith, Richard D

2013-03-01

For bottom-up proteomics, there are wide variety of database-searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid-search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection--referred to as STEPS--utilizes user-defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal "parameter set" for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true-positive identifications are demonstrated using datasets derived from immunoaffinity-depleted blood serum and a bacterial cell lysate, two common proteomics sample types. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

GWFASTA: server for FASTA search in eukaryotic and microbial genomes.

PubMed

Issac, Biju; Raghava, G P S

2002-09-01

Similarity searches are a powerful method for solving important biological problems such as database scanning, evolutionary studies, gene prediction, and protein structure prediction. FASTA is a widely used sequence comparison tool for rapid database scanning. Here we describe the GWFASTA server that was developed to assist the FASTA user in similarity searches against partially and/or completely sequenced genomes. GWFASTA consists of more than 60 microbial genomes, eight eukaryote genomes, and proteomes of annotatedgenomes. Infact, it provides the maximum number of databases for similarity searching from a single platform. GWFASTA allows the submission of more than one sequence as a single query for a FASTA search. It also provides integrated post-processing of FASTA output, including compositional analysis of proteins, multiple sequences alignment, and phylogenetic analysis. Furthermore, it summarizes the search results organism-wise for prokaryotes and chromosome-wise for eukaryotes. Thus, the integration of different tools for sequence analyses makes GWFASTA a powerful toolfor biologists.

Analysis of Users' Searches of CD-ROM Databases in the National and University Library in Zagreb.

ERIC Educational Resources Information Center

Jokic, Maja

1997-01-01

Investigates the search behavior of CD-ROM database users in Zagreb (Croatia) libraries: one group needed a minimum of technical assistance, and the other was completely independent. Highlights include the use of questionnaires and transaction log analysis and the need for end-user education. The questionnaire and definitions of search process…

Methodological Quality Assessment of Meta-analyses in Endodontics.

PubMed

Kattan, Sereen; Lee, Su-Min; Kohli, Meetu R; Setzer, Frank C; Karabucak, Bekir

2018-01-01

The objectives of this review were to assess the methodological quality of published meta-analyses related to endodontics using the assessment of multiple systematic reviews (AMSTAR) tool and to provide a follow-up to previously published reviews. Three electronic databases were searched for eligible studies according to the inclusion and exclusion criteria: Embase via Ovid, The Cochrane Library, and Scopus. The electronic search was amended by a hand search of 6 dental journals (International Endodontic Journal; Journal of Endodontics; Australian Endodontic Journal; Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology; Endodontics and Dental Traumatology; and Journal of Dental Research). The searches were conducted to include articles published after July 2009, and the deadline for inclusion of the meta-analyses was November 30, 2016. The AMSTAR assessment tool was used to evaluate the methodological quality of all included studies. A total of 36 reports of meta-analyses were included. The overall quality of the meta-analyses reports was found to be medium, with an estimated mean overall AMSTAR score of 7.25 (95% confidence interval, 6.59-7.90). The most poorly assessed areas were providing an a priori design, the assessment of the status of publication, and publication bias. In recent publications in the field of endodontics, the overall quality of the reported meta-analyses is medium according to AMSTAR. Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Mandibular single-implant overdentures: a review with surgical and prosthodontic perspectives of a novel approach.

PubMed

Alsabeeha, Nabeel; Payne, Alan G T; De Silva, Rohana K; Swain, Michael V

2009-04-01

To review the literature on mandibular single-implant overdentures (opposing complete maxillary dentures), and present surgical and prosthodontic perspectives of a novel approach for this treatment option. An electronic search through the databases of Pubmed, Embase and Medline using the linked key words 'mandibular single implant overdentures' was performed. The search was limited to English language articles published up to August 2008. Hand searches through articles retrieved from the electronic search, peer-reviewed journals and recent conference proceedings were also conducted. A limited number of reports were identified on mandibular single-implant overdentures (opposing maxillary complete dentures). They comprised of case-series reports, short-term prospective trials and current randomized-controlled clinical trials. Different loading protocols with different implant systems have been used, but always with regular diameter implants. Specific anatomical and vascular dangers of the mandibular midline symphysis are identified including a novel surgical approach using a currently available short, wide diameter tapered implant. In addition, the prosthodontic rationale for using a larger attachment system (incorporating a platform switch) for mandibular single-implant overdentures is described. The review reveals that there is a lack of published randomized clinical trials using mandibular single-implant overdentures, opposing maxillary complete dentures. Without the evidence from randomized clinical trials, routine use of this novel approach cannot be recommended, compared with using regular diameter implants and matching attachment systems.

Osteoarthritis year in review 2015: rehabilitation and outcomes.

PubMed

Bennell, K L; Hall, M; Hinman, R S

2016-01-01

The purpose of this narrative review was to highlight recent research in the rehabilitation of people with osteoarthritis (OA) by summarizing findings from selected key systematic reviews and randomized controlled trials (RCTs). A systematic search was conducted using the PubMed, Physiotherapy Evidence Database (PEDro) and Cochrane databases from April 1st 2014 to March 31st 2015. A selection of these is discussed based on study quality, relevance, contribution to new knowledge or controversial findings. Methodological quality of RCTs was assessed using guidelines from PEDro. From 274 articles, 74 were deemed to meet the eligibility criteria including 24 systematic reviews and 50 studies reporting on findings from RCTs. Overall the methodological quality of the RCTs was moderate. The studies were grouped into several themes covering; evidence of rehabilitation outcomes in less studied joints including the hand and hip; new insights into exercise in knee OA; effects of biomechanical treatments on symptoms and structure in knee OA; and effects of acupuncture. Exercise was the most common treatment evaluated. Although little evidence supported benefit of exercise for hand OA, exercise has positive effects for hip and knee OA symptoms and these benefits may depend upon patient phenotypes. The first evidence that a brace can influence knee joint structure emerged. The latest evidence suggests that acupuncture has, at best, small treatment effects on knee OA pain of unlikely clinical relevance. Copyright © 2015 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Revisiting reflexology: Concept, evidence, current practice, and practitioner training.

PubMed

Embong, Nurul Haswani; Soh, Yee Chang; Ming, Long Chiau; Wong, Tin Wui

2015-10-01

Reflexology is basically a study of how one part of the human body relates to another part of the body. Reflexology practitioners rely on the reflexes map of the feet and hands to all the internal organs and other human body parts. They believe that by applying the appropriate pressure and massage certain spots on the feet and hands, all other body parts could be energized and rejuvenated. This review aimed to revisit the concept of reflexology and examine its effectiveness, practices, and the training for reflexology practitioners. PubMed, SCOPUS, Google Scholar, and SpringerLink databases were utilized to search the following medical subject headings or keywords: foot massage, reflexology, foot reflexotherapy, reflexological treatment, and zone therapy. The articles published for the last 10 years were included. Previous systematic reviews failed to show concrete evidence for any specific effect of reflexology in any conditions. Due to its non-invasive, non-pharmacological complementary nature, reflexology is widely accepted and anecdotal evidence of positive effect reflexology in a variety of health conditions are available. Adequate training for practitioners is necessary to ensure the consistency of service provided.

Revisiting reflexology: Concept, evidence, current practice, and practitioner training

PubMed Central

Embong, Nurul Haswani; Soh, Yee Chang; Ming, Long Chiau; Wong, Tin Wui

2015-01-01

Reflexology is basically a study of how one part of the human body relates to another part of the body. Reflexology practitioners rely on the reflexes map of the feet and hands to all the internal organs and other human body parts. They believe that by applying the appropriate pressure and massage certain spots on the feet and hands, all other body parts could be energized and rejuvenated. This review aimed to revisit the concept of reflexology and examine its effectiveness, practices, and the training for reflexology practitioners. PubMed, SCOPUS, Google Scholar, and SpringerLink databases were utilized to search the following medical subject headings or keywords: foot massage, reflexology, foot reflexotherapy, reflexological treatment, and zone therapy. The articles published for the last 10 years were included. Previous systematic reviews failed to show concrete evidence for any specific effect of reflexology in any conditions. Due to its non-invasive, non-pharmacological complementary nature, reflexology is widely accepted and anecdotal evidence of positive effect reflexology in a variety of health conditions are available. Adequate training for practitioners is necessary to ensure the consistency of service provided. PMID:26587391

Databases and archiving for cryoEM

PubMed Central

Patwardhan, Ardan; Lawson, Catherine L.

2017-01-01

Cryo-EM in structural biology is currently served by three public archives – EMDB for 3DEM reconstructions, PDB for models built from 3DEM reconstructions and EMPIAR for the raw 2D image data used to obtain the 3DEM reconstructions. These archives play a vital role for both the structural community and the wider biological community in making the data accessible so that results may be reused, reassessed and integrated with other structural and bioinformatics resources. The important role of the archives is underpinned by the fact that many journals mandate the deposition of data to PDB and EMDB on publication. The field is currently undergoing transformative changes where on the one hand high-resolution structures are becoming a routine occurrence while on the other hand electron tomography is enabling the study of macromolecules in the cellular context. Concomitantly the archives are evolving to best serve their stakeholder communities. In this chapter we describe the current state of the archives, resources available for depositing, accessing, searching, visualising and validating data, on-going community-wide initiatives and opportunities and challenges for the future. PMID:27572735

Systematic review of the effects of mirror therapy in children with cerebral palsy.

PubMed

Park, Eom-Ji; Baek, Soon-Hyung; Park, Soohee

2016-11-01

[Purpose] To provide data for systematic intervention plans in occupational therapy practice by objectivity showing the value of mirror therapy interventions in children with cerebral palsy. [Subjects and Methods] Medline and EMBASE databases were searched for the key words "cerebral palsy," "mirror movement," "mirror therapy," and "mirror visual feedback." Nine studies that met the inclusion and exclusion criteria were identified. The qualitatively determined level of evidence, period of research, comparisons and interventions, tools used to measure the intervention, and the effects were analyzed. [Results] According to the results analyzed, one (1/9, 11.1%) study showed the same result as the control group, one (1/9, 11.1%) showed a negative effect, and seven (7/9, 77.8%) showed positive effects of mirror-mediated therapy, with meaningful improvement in function, such as hand strength, movement speed, muscle activity, and accuracy of hand matching. [Conclusion] Through this study, the value of mirror-mediated therapeutic interventions in occupational therapy practice targeting cerebral palsy was confirmed. It is expected that this result will be useful in establishing mirror therapy as an interventional program.

The effect of surface tension reduction on the clinical performance of sodium hypochlorite in endodontics.

PubMed

Rossi-Fedele, G; Prichard, J W; Steier, L; de Figueiredo, J A P

2013-06-01

Sodium hypochlorite (NaOCl) is recommended as an endodontic irrigant in view of its broad antimicrobial and tissue dissolution capacities. To enhance its penetration into inaccessible areas of root canals and to improve its overall effect, the addition of surface-active agents has been suggested. The aim of this investigation was to review the effect of the reduction of the surface tension on the performance of NaOCl in endodontics. A search was performed in the Medline electronic database (articles published up to 28 July 2012, in English) with the search terms and combinations as follows: 'sodium hypochlorite AND surface tension or interfacial force or interfacial tension or surface-active agent or amphiphilic agent or surface active agent or surfactant or tenside or detergent'. The purpose of this search was to identify publications that compared NaOCl alone and NaOCl modified with the addition of a surface-active agent in endodontics. A hand search of articles published online ('in-press' and 'early view'), and appearing in the reference list of the articles included, was further performed, using the same search criteria as the electronic search. The search identified 302 publications, of which 11 fulfilled the inclusion/exclusion criteria of the review. The evidence available suggests that surface-active agents improve the penetration of NaOCl in the main canal and have no effect on its pulp tissue dissolution ability. There are, however, insufficient data to enable a sound conclusion to be drawn regarding the effect of modifying NaOCl's surface tension on lubrication, antimicrobial and smear layer or debris removal abilities. © 2012 International Endodontic Journal.

Tautomerism in chemical information management systems

NASA Astrophysics Data System (ADS)

Warr, Wendy A.

2010-06-01

Tautomerism has an impact on many of the processes in chemical information management systems including novelty checking during registration into chemical structure databases; storage of structures; exact and substructure searching in chemical structure databases; and depiction of structures retrieved by a search. The approaches taken by 27 different software vendors and database producers are compared. It is hoped that this comparison will act as a discussion document that could ultimately improve databases and software for researchers in the future.

Searching the ASRS Database Using QUORUM Keyword Search, Phrase Search, Phrase Generation, and Phrase Discovery

NASA Technical Reports Server (NTRS)

McGreevy, Michael W.; Connors, Mary M. (Technical Monitor)

2001-01-01

To support Search Requests and Quick Responses at the Aviation Safety Reporting System (ASRS), four new QUORUM methods have been developed: keyword search, phrase search, phrase generation, and phrase discovery. These methods build upon the core QUORUM methods of text analysis, modeling, and relevance-ranking. QUORUM keyword search retrieves ASRS incident narratives that contain one or more user-specified keywords in typical or selected contexts, and ranks the narratives on their relevance to the keywords in context. QUORUM phrase search retrieves narratives that contain one or more user-specified phrases, and ranks the narratives on their relevance to the phrases. QUORUM phrase generation produces a list of phrases from the ASRS database that contain a user-specified word or phrase. QUORUM phrase discovery finds phrases that are related to topics of interest. Phrase generation and phrase discovery are particularly useful for finding query phrases for input to QUORUM phrase search. The presentation of the new QUORUM methods includes: a brief review of the underlying core QUORUM methods; an overview of the new methods; numerous, concrete examples of ASRS database searches using the new methods; discussion of related methods; and, in the appendices, detailed descriptions of the new methods.

Clostridium difficile contamination of health care workers' hands and its potential contribution to the spread of infection: Review of the literature.

PubMed

Jullian-Desayes, Ingrid; Landelle, Caroline; Mallaret, Marie-Reine; Brun-Buisson, Christian; Barbut, Frédéric

2017-01-01

Clostridium difficile infection (CDI) can be transmitted from patient to patient by the hands of health care workers (HCWs); however, the relative importance of this route in the spread of C difficile in the hospital is currently unknown. Our aim was to review studies examining HCWs' hand carriage and its potential role in CDI transmission. First, English-speaking references addressing HCWs' hand sampling obtained from the PubMed database were reviewed. Second, C difficile outbreaks definitely or probably implicating HCWs were retrieved from the Outbreak Database Web site (www.outbreak-database.com). Finally, cases of C difficile occurring in HCWs after contact with an infected patient were retrieved from PubMed. A total of 11 studies dealing with HCWs' hand carriage were selected and reviewed. Between 0% and 59% of HCWs' hands were found contaminated with C difficile after caring for a patient with CDI. There were several differences between studies regarding site of hands sampling, timing after contact, and bacteriologic methods. Only 2 C difficile outbreaks implicating HCWs and 6 series of cases of transmission from patients to HCWs have been reported. This review shows that HCWs' hands could play an important role in the transmission of C difficile. Hand hygiene and reduction of environmental contamination are essential to control C difficile transmission. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Pediatric ingestions of house hold products containing ethanol: a review.

PubMed

Rayar, Praveen; Ratnapalan, Savithiri

2013-03-01

Alcohol is present in a number of household items that are readily accessible to children. Ingestion of these household products containing alcohol can lead to significant health risks. To identify reported cases of ingestions of common household items that have led to ethanol intoxication, poisoning, or death in children up to the age of 18 years. The OVID MEDLINE database from 1948 to March 2011, Embase from 1980 to March 2011, and CINAHL (Cumulative Index to Nursing and Allied Health Literature) from 1982 to February 2011 were searched for articles with the following key terms: alcohols(ethanol or ethyl alcohol) and ingest*(ingestion) or intoxic*(intoxication) or poisoning* or death. The search was limited to children (0-18 years). All articles that reported ingestion of household products that contained ethanol were included in the analysis. Results. Many household products, particularly mouthwashes, hand sanitizers, and cosmetics contain quantities of ethanol that are significant enough to induce intoxication and hypoglycemia. There were 17 publications directly reporting on children with alcohol intoxication from household products. Serious adverse events included hypoglycemia, seizures, and death. Child-resistant closures appear to have reduced the incidence of ingestion of ethanol-based products, including mouthwashes, and may be applicable to other products such as hand sanitizers. Ingestion of household substances containing alcohol continues to be a health care problem. Legislature to reduce alcohol content in household products and public education should be instituted to prevent poisonings in children.

Mass measurement errors of Fourier-transform mass spectrometry (FTMS): distribution, recalibration, and application.

PubMed

Zhang, Jiyang; Ma, Jie; Dou, Lei; Wu, Songfeng; Qian, Xiaohong; Xie, Hongwei; Zhu, Yunping; He, Fuchu

2009-02-01

The hybrid linear trap quadrupole Fourier-transform (LTQ-FT) ion cyclotron resonance mass spectrometer, an instrument with high accuracy and resolution, is widely used in the identification and quantification of peptides and proteins. However, time-dependent errors in the system may lead to deterioration of the accuracy of these instruments, negatively influencing the determination of the mass error tolerance (MET) in database searches. Here, a comprehensive discussion of LTQ/FT precursor ion mass error is provided. On the basis of an investigation of the mass error distribution, we propose an improved recalibration formula and introduce a new tool, FTDR (Fourier-transform data recalibration), that employs a graphic user interface (GUI) for automatic calibration. It was found that the calibration could adjust the mass error distribution to more closely approximate a normal distribution and reduce the standard deviation (SD). Consequently, we present a new strategy, LDSF (Large MET database search and small MET filtration), for database search MET specification and validation of database search results. As the name implies, a large-MET database search is conducted and the search results are then filtered using the statistical MET estimated from high-confidence results. By applying this strategy to a standard protein data set and a complex data set, we demonstrate the LDSF can significantly improve the sensitivity of the result validation procedure.

G-Hash: Towards Fast Kernel-based Similarity Search in Large Graph Databases.

PubMed

Wang, Xiaohong; Smalter, Aaron; Huan, Jun; Lushington, Gerald H

2009-01-01

Structured data including sets, sequences, trees and graphs, pose significant challenges to fundamental aspects of data management such as efficient storage, indexing, and similarity search. With the fast accumulation of graph databases, similarity search in graph databases has emerged as an important research topic. Graph similarity search has applications in a wide range of domains including cheminformatics, bioinformatics, sensor network management, social network management, and XML documents, among others.Most of the current graph indexing methods focus on subgraph query processing, i.e. determining the set of database graphs that contains the query graph and hence do not directly support similarity search. In data mining and machine learning, various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models for supervised learning, graph kernel functions have (i) high computational complexity and (ii) non-trivial difficulty to be indexed in a graph database.Our objective is to bridge graph kernel function and similarity search in graph databases by proposing (i) a novel kernel-based similarity measurement and (ii) an efficient indexing structure for graph data management. Our method of similarity measurement builds upon local features extracted from each node and their neighboring nodes in graphs. A hash table is utilized to support efficient storage and fast search of the extracted local features. Using the hash table, a graph kernel function is defined to capture the intrinsic similarity of graphs and for fast similarity query processing. We have implemented our method, which we have named G-hash, and have demonstrated its utility on large chemical graph databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Most importantly, the new similarity measurement and the index structure is scalable to large database with smaller indexing size, faster indexing construction time, and faster query processing time as compared to state-of-the-art indexing methods such as C-tree, gIndex, and GraphGrep.

Cost and Search Result Comparisons of BRS After Dark and Knowledge Index.

ERIC Educational Resources Information Center

Cloud, Gayla Staples; Hambric, Jacqueline

This two-part study was designed (1) to determine differences in the costs of searching BRS After Dark (BRS AD) and Knowledge Index (KI) generally and across ten selected databases, and (2) to determine whether there is a difference in the citations retrieved when the same search is conducted on the same database in both systems. Study methodology…

PubMed searches: overview and strategies for clinicians.

PubMed

Lindsey, Wesley T; Olin, Bernie R

2013-04-01

PubMed is a biomedical and life sciences database maintained by a division of the National Library of Medicine known as the National Center for Biotechnology Information (NCBI). It is a large resource with more than 5600 journals indexed and greater than 22 million total citations. Searches conducted in PubMed provide references that are more specific for the intended topic compared with other popular search engines. Effective PubMed searches allow the clinician to remain current on the latest clinical trials, systematic reviews, and practice guidelines. PubMed continues to evolve by allowing users to create a customized experience through the My NCBI portal, new arrangements and options in search filters, and supporting scholarly projects through exportation of citations to reference managing software. Prepackaged search options available in the Clinical Queries feature also allow users to efficiently search for clinical literature. PubMed also provides information regarding the source journals themselves through the Journals in NCBI Databases link. This article provides an overview of the PubMed database's structure and features as well as strategies for conducting an effective search.

Hand hygiene monitoring technology: protocol for a systematic review

PubMed Central

2013-01-01

Background Healthcare worker hand hygiene is thought to be one of the most important strategies to prevent healthcare-associated infections, but compliance is generally poor. Hand hygiene improvement interventions must include audits of compliance (almost always with feedback), which are most often done by direct observation - a method that is expensive, subjective, and prone to bias. New technologies, including electronic and video hand hygiene monitoring systems, have the potential to provide continuous and objective monitoring of hand hygiene, regular feedback, and for some systems, real-time reminders. We propose a systematic review of the evidence supporting the effectiveness of these systems. The primary objective is to determine whether hand hygiene monitoring systems yield sustainable improvements in hand hygiene compliance when compared to usual care. Methods/Design MEDLINE, EMBASE, CINAHL, and other relevant databases will be searched for randomized control studies and quasi-experimental studies evaluating a video or electronic hand hygiene monitoring system. A standard data collection form will be used to abstract relevant information from included studies. Bias will be assessed using the Cochrane Effective Practice and Organization of Care Group Risk of Bias Assessment Tool. Studies will be reviewed independently by two reviewers, with disputes resolved by a third reviewer. The primary outcome is directly observed hand hygiene compliance. Secondary outcomes include healthcare-associated infection incidence and improvements in hand hygiene compliance as measured by alternative metrics. Results will be qualitatively summarized with comparisons made between study quality, the measured outcome, and study-specific factors that may be expected to affect outcome (for example, study duration, frequency of feedback, use of real-time reminders). Meta-analysis will be performed if there is more than one study of similar systems with comparable outcome definitions. Discussion Electronic and video monitoring systems have the potential to improve hand hygiene compliance and prevent healthcare-associated infection, but are expensive, difficult to install and maintain, and may not be accepted by all healthcare workers. This review will assess the current evidence of effectiveness of these systems before their widespread adoption. Study registration PROSPERO registration number: CRD42013004519 PMID:24219817

Effects of rehabilitative interventions on pain, function and physical impairments in people with hand osteoarthritis: a systematic review

PubMed Central

2011-01-01

Introduction Hand osteoarthritis (OA) is associated with pain, reduced grip strength, loss of range of motion and joint stiffness leading to impaired hand function and difficulty with daily activities. The effectiveness of different rehabilitation interventions on specific treatment goals has not yet been fully explored. The objective of this systematic review is to provide evidence based knowledge on the treatment effects of different rehabilitation interventions for specific treatment goals for hand OA. Methods A computerized literature search of Medline, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), ISI Web of Science, the Physiotherapy Evidence Database (PEDro) and SCOPUS was performed. Studies that had an evidence level of 2b or higher and that compared a rehabilitation intervention with a control group and assessed at least one of the following outcome measures - pain, physical hand function or other measures of hand impairment - were included. The eligibility and methodological quality of trials were systematically assessed by two independent reviewers using the PEDro scale. Treatment effects were calculated using standardized mean difference and 95% confidence intervals. Results Ten studies, of which six were of higher quality (PEDro score >6), were included. The rehabilitation techniques reviewed included three studies on exercise, two studies each on laser and heat, and one study each on splints, massage and acupuncture. One higher quality trial showed a large positive effect of 12-month use of a night splint on hand pain, function, strength and range of motion. Exercise had no effect on hand pain or function although it may be able to improve hand strength. Low level laser therapy may be useful for improving range of motion. No rehabilitation interventions were found to improve stiffness. Conclusions There is emerging high quality evidence to support that rehabilitation interventions can offer significant benefits to individuals with hand OA. A summary of the higher quality evidence is provided to assist with clinical decision making based on current evidence. Further high-quality research is needed concerning the effects of rehabilitation interventions on specific treatment goals for hand OA. PMID:21332991

Hand hygiene monitoring technology: protocol for a systematic review.

PubMed

Srigley, Jocelyn A; Lightfoot, David; Fernie, Geoff; Gardam, Michael; Muller, Matthew P

2013-11-12

Healthcare worker hand hygiene is thought to be one of the most important strategies to prevent healthcare-associated infections, but compliance is generally poor. Hand hygiene improvement interventions must include audits of compliance (almost always with feedback), which are most often done by direct observation - a method that is expensive, subjective, and prone to bias. New technologies, including electronic and video hand hygiene monitoring systems, have the potential to provide continuous and objective monitoring of hand hygiene, regular feedback, and for some systems, real-time reminders. We propose a systematic review of the evidence supporting the effectiveness of these systems. The primary objective is to determine whether hand hygiene monitoring systems yield sustainable improvements in hand hygiene compliance when compared to usual care. MEDLINE, EMBASE, CINAHL, and other relevant databases will be searched for randomized control studies and quasi-experimental studies evaluating a video or electronic hand hygiene monitoring system. A standard data collection form will be used to abstract relevant information from included studies. Bias will be assessed using the Cochrane Effective Practice and Organization of Care Group Risk of Bias Assessment Tool. Studies will be reviewed independently by two reviewers, with disputes resolved by a third reviewer. The primary outcome is directly observed hand hygiene compliance. Secondary outcomes include healthcare-associated infection incidence and improvements in hand hygiene compliance as measured by alternative metrics. Results will be qualitatively summarized with comparisons made between study quality, the measured outcome, and study-specific factors that may be expected to affect outcome (for example, study duration, frequency of feedback, use of real-time reminders). Meta-analysis will be performed if there is more than one study of similar systems with comparable outcome definitions. Electronic and video monitoring systems have the potential to improve hand hygiene compliance and prevent healthcare-associated infection, but are expensive, difficult to install and maintain, and may not be accepted by all healthcare workers. This review will assess the current evidence of effectiveness of these systems before their widespread adoption. PROSPERO registration number: CRD42013004519.

An ontology-based search engine for protein-protein interactions

PubMed Central

2010-01-01

Background Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. Results We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Conclusion Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology. PMID:20122195

An ontology-based search engine for protein-protein interactions.

PubMed

Park, Byungkyu; Han, Kyungsook

2010-01-18

Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology.

Using the Turning Research Into Practice (TRIP) database: how do clinicians really search?*

PubMed Central

Meats, Emma; Brassey, Jon; Heneghan, Carl; Glasziou, Paul

2007-01-01

Objectives: Clinicians and patients are increasingly accessing information through Internet searches. This study aimed to examine clinicians' current search behavior when using the Turning Research Into Practice (TRIP) database to examine search engine use and the ways it might be improved. Methods: A Web log analysis was undertaken of the TRIP database—a meta-search engine covering 150 health resources including MEDLINE, The Cochrane Library, and a variety of guidelines. The connectors for terms used in searches were studied, and observations were made of 9 users' search behavior when working with the TRIP database. Results: Of 620,735 searches, most used a single term, and 12% (n = 75,947) used a Boolean operator: 11% (n = 69,006) used “AND” and 0.8% (n = 4,941) used “OR.” Of the elements of a well-structured clinical question (population, intervention, comparator, and outcome), the population was most commonly used, while fewer searches included the intervention. Comparator and outcome were rarely used. Participants in the observational study were interested in learning how to formulate better searches. Conclusions: Web log analysis showed most searches used a single term and no Boolean operators. Observational study revealed users were interested in conducting efficient searches but did not always know how. Therefore, either better training or better search interfaces are required to assist users and enable more effective searching. PMID:17443248

LiverTox: Clinical and Research Information on Drug-Induced Liver Injury

MedlinePlus

... News Information Resources Glossary Abbreviations SEARCH THE LIVERTOX DATABASE Search for a specific medication, herbal or supplement: ... About Us . Disclaimer. Information presented in the LiverTox database is derived from the scientific literature and public ...

A comparison of the performance of seven key bibliographic databases in identifying all relevant systematic reviews of interventions for hypertension.

PubMed

Rathbone, John; Carter, Matt; Hoffmann, Tammy; Glasziou, Paul

2016-02-09

Bibliographic databases are the primary resource for identifying systematic reviews of health care interventions. Reliable retrieval of systematic reviews depends on the scope of indexing used by database providers. Therefore, searching one database may be insufficient, but it is unclear how many need to be searched. We sought to evaluate the performance of seven major bibliographic databases for the identification of systematic reviews for hypertension. We searched seven databases (Cochrane library, Database of Abstracts of Reviews of Effects (DARE), Excerpta Medica Database (EMBASE), Epistemonikos, Medical Literature Analysis and Retrieval System Online (MEDLINE), PubMed Health and Turning Research Into Practice (TRIP)) from 2003 to 2015 for systematic reviews of any intervention for hypertension. Citations retrieved were screened for relevance, coded and checked for screening consistency using a fuzzy text matching query. The performance of each database was assessed by calculating its sensitivity, precision, the number of missed reviews and the number of unique records retrieved. Four hundred systematic reviews were identified for inclusion from 11,381 citations retrieved from seven databases. No single database identified all the retrieved systematic reviews for hypertension. EMBASE identified the most reviews (sensitivity 69 %) but also retrieved the most irrelevant citations with 7.2 % precision (Pr). The sensitivity of the Cochrane library was 60 %, DARE 57 %, MEDLINE 57 %, PubMed Health 53 %, Epistemonikos 49 % and TRIP 33 %. EMBASE contained the highest number of unique records (n = 43). The Cochrane library identified seven unique records and had the highest precision (Pr = 30 %), followed by Epistemonikos (n = 2, Pr = 19 %). No unique records were found in PubMed Health (Pr = 24 %) DARE (Pr = 21 %), TRIP (Pr = 10 %) or MEDLINE (Pr = 10 %). Searching EMBASE and the Cochrane library identified 88 % of all systematic reviews in the reference set, and searching the freely available databases (Cochrane, Epistemonikos, MEDLINE) identified 83 % of all the reviews. The databases were re-analysed after systematic reviews of non-conventional interventions (e.g. yoga, acupuncture) were removed. Similarly, no database identified all the retrieved systematic reviews. EMBASE identified the most relevant systematic reviews (sensitivity 73 %) but also retrieved the most irrelevant citations with Pr = 5 %. The sensitivity of the Cochrane database was 62 %, followed by MEDLINE (60 %), DARE (55 %), PubMed Health (54 %), Epistemonikos (50 %) and TRIP (31 %). The precision of the Cochrane library was the highest (20 %), followed by PubMed Health (Pr = 16 %), DARE (Pr = 13 %), Epistemonikos (Pr = 12 %), MEDLINE (Pr = 6 %), TRIP (Pr = 6 %) and EMBASE (Pr = 5 %). EMBASE contained the most unique records (n = 34). The Cochrane library identified seven unique records. The other databases held no unique records. The coverage of bibliographic databases varies considerably due to differences in their scope and content. Researchers wishing to identify systematic reviews should not rely on one database but search multiple databases.

The role of patient isolation and compliance with isolation practices in the control of nosocomial MRSA in acute care.

PubMed

Halcomb, Elizabeth J; Griffiths, Rhonda; Fernandez, Ritin

2008-06-01

Background  Nosocomial infection remains the most common complication of hospitalisation. Despite infection control efforts, nosocomial methicillin resistant Staphylococcus aureus (MRSA) transmission continues to rise. Various isolation practices are used to minimise MRSA transmission in acute care. However, the effectiveness of these practices has seldom been evaluated. Objectives  This review sought to evaluate the efficacy of isolation practices in minimising MRSA transmission in the acute hospital setting and explore staff, visitor and patient compliance with isolation practices. This review updates a review published in 2002. Search strategy  A systematic search for relevant published or unpublished English language literature was undertaken using electronic databases, the reference lists of retrieved papers and the Internet. This extended the search published in the original review. Databases searched included: Medline, CINAHL, EMBASE, Cochrane Library and Joanna Briggs Institute Evidence Library. Selection criteria  All English language research reports published between 1990 and August 2005 that focused on the role of isolation practices on the nosocomial transmission of MRSA in adult, paediatric or neonatal acute care settings were eligible for inclusion in the review. Studies that evaluated multiple infection control strategies or control of MRSA outbreaks were excluded. The main outcome of interest was the incidence of new cases of MRSA. The secondary outcome was staff, visitor and patient compliance with the isolation practices. Data collection and analysis  Two reviewers assessed each paper against the inclusion criteria and a validated quality scale. Data extraction was undertaken using a tool designed specifically for this review. Statistical comparisons of findings were not possible, so findings are presented in a narrative form. Results  Seven studies met the inclusion criteria. Given the small number of included studies and variable methodological quality, care must be taken when interpreting the review findings. There is some evidence that cessation of single room isolation and cohorting of MRSA patients does not increase nosocomial MRSA transmission when hand-washing compliance and standard precautions are maintained. Indeed, there is some evidence that reduced MRSA transmission can be achieved by improving compliance with contact precautions alone. The low level of hand hygiene compliance reported in the literature suggests that staff compliance with isolation practices is a significant factor in evaluating any infection-controlled intervention in the clinical setting. While staff compliance data are conflicting, regular audit and feedback of performance may improve compliance. Implications for clinical practice  The heterogeneous nature of the topic and methodological weaknesses of included studies impairs the ability to aggregate data and develop specific practice recommendations. While this review presents evidence to suggest that ceasing single room or cohort isolation does not lead to increased MRSA transmission, these studies maintained high levels of hand hygiene or standard precautions. Additionally, the role of extraneous factors, such as environmental reservoirs, specific MRSA strains and patient mix, is unclear. None of the included studies measured financial, social or psychological factors associated with isolation practices. There is an urgent need for well-designed research with significant sample sizes to develop an evidence base upon which to underpin future clinical practice. © 2008 The Authors. Journal Compilation © Blackwell Publishing Asia Pty Ltd.

Information Retrieval in Telemedicine: a Comparative Study on Bibliographic Databases

PubMed Central

Ahmadi, Maryam; Sarabi, Roghayeh Ershad; Orak, Roohangiz Jamshidi; Bahaadinbeigy, Kambiz

2015-01-01

Background and Aims: The first step in each systematic review is selection of the most valid database that can provide the highest number of relevant references. This study was carried out to determine the most suitable database for information retrieval in telemedicine field. Methods: Cinhal, PubMed, Web of Science and Scopus databases were searched for telemedicine matched with Education, cost benefit and patient satisfaction. After analysis of the obtained results, the accuracy coefficient, sensitivity, uniqueness and overlap of databases were calculated. Results: The studied databases differed in the number of retrieved articles. PubMed was identified as the most suitable database for retrieving information on the selected topics with the accuracy and sensitivity ratios of 50.7% and 61.4% respectively. The uniqueness percent of retrieved articles ranged from 38% for Pubmed to 3.0% for Cinhal. The highest overlap rate (18.6%) was found between PubMed and Web of Science. Less than 1% of articles have been indexed in all searched databases. Conclusion: PubMed is suggested as the most suitable database for starting search in telemedicine and after PubMed, Scopus and Web of Science can retrieve about 90% of the relevant articles. PMID:26236086

Information Retrieval in Telemedicine: a Comparative Study on Bibliographic Databases.

PubMed

Ahmadi, Maryam; Sarabi, Roghayeh Ershad; Orak, Roohangiz Jamshidi; Bahaadinbeigy, Kambiz

2015-06-01

The first step in each systematic review is selection of the most valid database that can provide the highest number of relevant references. This study was carried out to determine the most suitable database for information retrieval in telemedicine field. Cinhal, PubMed, Web of Science and Scopus databases were searched for telemedicine matched with Education, cost benefit and patient satisfaction. After analysis of the obtained results, the accuracy coefficient, sensitivity, uniqueness and overlap of databases were calculated. The studied databases differed in the number of retrieved articles. PubMed was identified as the most suitable database for retrieving information on the selected topics with the accuracy and sensitivity ratios of 50.7% and 61.4% respectively. The uniqueness percent of retrieved articles ranged from 38% for Pubmed to 3.0% for Cinhal. The highest overlap rate (18.6%) was found between PubMed and Web of Science. Less than 1% of articles have been indexed in all searched databases. PubMed is suggested as the most suitable database for starting search in telemedicine and after PubMed, Scopus and Web of Science can retrieve about 90% of the relevant articles.

Prairie Resources

Science.gov Websites

Search Prairie Resources for Students Plant Database Plant Database Butterfly Info Butterfly Info Insects Insect Database Frogs Frog Info Bird Database Bird Database Online Prairie Data Online Prairie Data

The use of Research Electronic Data Capture (REDCap) software to create a database of librarian-mediated literature searches.

PubMed

Lyon, Jennifer A; Garcia-Milian, Rolando; Norton, Hannah F; Tennant, Michele R

2014-01-01

Expert-mediated literature searching, a keystone service in biomedical librarianship, would benefit significantly from regular methodical review. This article describes the novel use of Research Electronic Data Capture (REDCap) software to create a database of literature searches conducted at a large academic health sciences library. An archive of paper search requests was entered into REDCap, and librarians now prospectively enter records for current searches. Having search data readily available allows librarians to reuse search strategies and track their workload. In aggregate, this data can help guide practice and determine priorities by identifying users' needs, tracking librarian effort, and focusing librarians' continuing education.

Effectiveness of interceptive treatment of class III malocclusions with skeletal anchorage: A systematic review and meta-analysis.

PubMed

Rodríguez de Guzmán-Barrera, Jorge; Sáez Martínez, Carla; Boronat-Catalá, Montserrat; Montiel-Company, Jose María; Paredes-Gallardo, Vanessa; Gandía-Franco, José Luís; Almerich-Silla, José Manuel; Bellot-Arcís, Carlos

2017-01-01

Recently, new strategies for treating class III malocclusions have appeared. Skeletal anchorage appears to reduce the dentoalveolar effects while maximising the orthopaedic effect in growing patients. The purpose of this systematic review and meta-analysis is to examine the effectiveness of bone anchorage devices for interceptive treatment of skeletal class III malocclusions. Searches were made in the Pubmed, Embase, Scopus and Cochrane databases, as well as in a grey literature database, and were complemented by hand-searching. The criteria for eligibility were: patients who had undergone orthodontic treatment with skeletal anchorage (miniplates and miniscrews). Patients with syndromes or craniofacial deformities or who had undergone maxillofacial surgery were excluded. The following variables were recorded for each article: author, year of publication, type of study, sample size, dropouts, demographic variables, treatment carried out, radiographic study (2D or 3D), follow-up time, and quality of the articles on the Newcastle-Ottawa Scale. The means and confidence intervals of the following variables were employed: Wits, overjet, ANB, SNA and SNB. Initially, 239 articles were identified. After removing the duplicates and applying the selection criteria, 9 were included in the qualitative synthesis and 7 in the quantitative synthesis (meta-analysis). It may be concluded that skeletal anchorage is an effective treatment for improving skeletal Class III malocclusion, but when compared with other traditional treatments such as disjunction and face mask, there is no clear evidence that skeletal anchorage improves the results.

Effectiveness of interceptive treatment of class III malocclusions with skeletal anchorage: A systematic review and meta-analysis

PubMed Central

Rodríguez de Guzmán-Barrera, Jorge; Sáez Martínez, Carla; Boronat-Catalá, Montserrat; Montiel-Company, Jose María; Paredes-Gallardo, Vanessa; Gandía-Franco, José Luís; Almerich-Silla, José Manuel; Bellot-Arcís, Carlos

2017-01-01

Recently, new strategies for treating class III malocclusions have appeared. Skeletal anchorage appears to reduce the dentoalveolar effects while maximising the orthopaedic effect in growing patients. The purpose of this systematic review and meta-analysis is to examine the effectiveness of bone anchorage devices for interceptive treatment of skeletal class III malocclusions. Searches were made in the Pubmed, Embase, Scopus and Cochrane databases, as well as in a grey literature database, and were complemented by hand-searching. The criteria for eligibility were: patients who had undergone orthodontic treatment with skeletal anchorage (miniplates and miniscrews). Patients with syndromes or craniofacial deformities or who had undergone maxillofacial surgery were excluded. The following variables were recorded for each article: author, year of publication, type of study, sample size, dropouts, demographic variables, treatment carried out, radiographic study (2D or 3D), follow-up time, and quality of the articles on the Newcastle-Ottawa Scale. The means and confidence intervals of the following variables were employed: Wits, overjet, ANB, SNA and SNB. Initially, 239 articles were identified. After removing the duplicates and applying the selection criteria, 9 were included in the qualitative synthesis and 7 in the quantitative synthesis (meta-analysis). It may be concluded that skeletal anchorage is an effective treatment for improving skeletal Class III malocclusion, but when compared with other traditional treatments such as disjunction and face mask, there is no clear evidence that skeletal anchorage improves the results. PMID:28328995

[The public health care system and rehabilitation actions in Brazil].

PubMed

Ribeiro, Carla Trevisan Martins; Ribeiro, Marcia Gonçalves; Araújo, Alexandra Prufer; Mello, Lívia Rodrigues; Rubim, Luciana da Cruz; Ferreira, Joyce Espírito Santo

2010-07-01

To produce a historical account of rehabilitation actions in the context of the Brazilian Unified Health Care System (SUS). Search of SciELO, LILACS, and MEDLINE databases for literature published between 1980 and 2009. The following Portuguese search terms were used: Sistema Unico de Saúde, reabilitação, políticas de saúde, assistência médica, história. The English terms "rehabilitation" and "public health" were also used. Federal laws and Ministry of Health manuals available at the city of Rio de Janeiro Coordinating Office for Rehabilitation Programs, Fundação Instituto Oswaldo Cruz library, and in BIREME database were also surveyed. Only a small number of publications were recovered (four books, three Health Ministry manuals, four articles published in Brazil, one master's thesis, and one doctoral dissertation). Nevertheless, analysis of these materials revealed that since many municipalities are still incapable of ensuring the right to universal and comprehensive health care, rehabilitation actions are often carried out in a precarious manner, unsupported by an adequate and comprehensive policy. On the other hand, there have been real improvements in terms of expanding care to the population with special needs. There still are factors hindering the achievement of optimal results in the care to people with special needs. The challenge of action planning must be undertaken especially by municipal governments to ensure an adequate supply of services and thus equity of access and comprehensive health care.

Patients’ experiences of chronic non-malignant musculoskeletal pain: a qualitative systematic review

PubMed Central

Toye, Francine; Seers, Kate; Allcock, Nick; Briggs, Michelle; Carr, Eloise; Andrews, JoyAnn; Barker, Karen

2013-01-01

Background Musculoskeletal (MSK) pain is one of the most predominant types of pain and accounts for a large portion of the primary care workload. Aim To systematically review and integrate the findings of qualitative research to increase understanding of patients’ experiences of chronic non-malignant MSK pain. Design and setting Synthesis of qualitative research using meta-ethnography using six electronic databases up until February 2012 (Medline, Embase, Cinahl, Psychinfo, Amed and HMIC). Method Databases were searched from their inception until February 2012, supplemented by hand-searching contents lists of specific journals for 2001–2011 and citation tracking. Full published reports of qualitative studies exploring adults’ own experience of chronic non-malignant MSK pain were eligible for inclusion. Results Out of 24 992 titles, 676 abstracts, and 321 full texts were screened, 77 papers reporting 60 individual studies were included. A new concept of pain as an adversarial struggle emerged. This adversarial struggle was to: 1) affirm self; 2) reconstruct self in time; 3) construct an explanation for suffering; 4) negotiate the healthcare system; and 5) prove legitimacy. However, despite this struggle there is also a sense for some patients of 6) moving forward alongside pain. Conclusions This review provides a theoretical underpinning for improving patient experience and facilitating a therapeutic collaborative partnership. A conceptual model is presented, which offers opportunities for improvement by involving patients, showing them their pain is understood, and forming the basis to help patients move forward alongside their pain. PMID:24351499

Efficient bibliographic searches on allergy using ISI databases.

PubMed

Sáez Gómez, J M; Annan, J W; Negro Alvarez, J M; Guillen-Grima, F; Bozzola, C M; Ivancevich, J C; Aguinaga Ontoso, E

2008-01-01

The aim of this article is to provide an introduction to using databases from the Thomson ISI Web of Knowledge, with special reference to Citation Indexes as an analysis tool for publications, and also to explain the meaning of the well-known Impact Factor. We present the partially modified new Consultation Interface to enhance information search routines of these databases. It introduces distinctive methods in search bibliography, including the correct application of analysis tools, paying particular attention to Journal Citation Reports and Impact Factor. We finish this article with comment on the consequences of using the Impact Factor as a quality indicator for the assessment of journals and publications, and how to ensure measures for indexing in the Thomson ISI Databases.

Identification of validated questionnaires to measure adherence to pharmacological antihypertensive treatments

PubMed Central

Pérez-Escamilla, Beatriz; Franco-Trigo, Lucía; Moullin, Joanna C; Martínez-Martínez, Fernando; García-Corpas, José P

2015-01-01

Background Low adherence to pharmacological treatments is one of the factors associated with poor blood pressure control. Questionnaires are an indirect measurement method that is both economic and easy to use. However, questionnaires should meet specific criteria, to minimize error and ensure reproducibility of results. Numerous studies have been conducted to design questionnaires that quantify adherence to pharmacological antihypertensive treatments. Nevertheless, it is unknown whether questionnaires fulfil the minimum requirements of validity and reliability. The aim of this study was to compile validated questionnaires measuring adherence to pharmacological antihypertensive treatments that had at least one measure of validity and one measure of reliability. Methods A literature search was undertaken in PubMed, the Excerpta Medica Database (EMBASE), and the Latin American and Caribbean Health Sciences Literature database (Literatura Latino-Americana e do Caribe em Ciências da Saúde [LILACS]). References from included articles were hand-searched. The included papers were all that were published in English, French, Portuguese, and Spanish from the beginning of the database’s indexing until July 8, 2013, where a validation of a questionnaire (at least one demonstration of the validity and at least one of reliability) was performed to measure adherence to antihypertensive pharmacological treatments. Results A total of 234 potential papers were identified in the electronic database search; of these, 12 met the eligibility criteria. Within these 12 papers, six questionnaires were validated: the Morisky–Green–Levine; Brief Medication Questionnaire; Hill-Bone Compliance to High Blood Pressure Therapy Scale; Morisky Medication Adherence Scale; Treatment Adherence Questionnaire for Patients with Hypertension (TAQPH); and Martín–Bayarre–Grau. Questionnaire length ranged from four to 28 items. Internal consistency, assessed by Cronbach’s α, varied from 0.43 to 0.889. Additional statistical techniques utilized to assess the psychometric properties of the questionnaires varied greatly across studies. Conclusion At this stage, none of the six questionnaires included could be considered a gold standard. However, this revision will assist health professionals in the selection of the most appropriate tool for their individual circumstances. PMID:25926723

A systematic review and metaanalysis of energy intake and weight gain in pregnancy.

PubMed

Jebeile, Hiba; Mijatovic, Jovana; Louie, Jimmy Chun Yu; Prvan, Tania; Brand-Miller, Jennie C

2016-04-01

Gestational weight gain within the recommended range produces optimal pregnancy outcomes, yet many women exceed the guidelines. Official recommendations to increase energy intake by ∼ 1000 kJ/day in pregnancy may be excessive. To determine by metaanalysis of relevant studies whether greater increments in energy intake from early to late pregnancy corresponded to greater or excessive gestational weight gain. We systematically searched electronic databases for observational and intervention studies published from 1990 to the present. The databases included Ovid Medline, Cochrane Library, Excerpta Medica DataBASE (EMBASE), Cumulative Index to Nursing and Allied Health Literature (CINAHL), and Science Direct. In addition we hand-searched reference lists of all identified articles. Studies were included if they reported gestational weight gain and energy intake in early and late gestation in women of any age with a singleton pregnancy. Search also encompassed journals emerging from both developed and developing countries. Studies were individually assessed for quality based on the Quality Criteria Checklist obtained from the Evidence Analysis Manual: Steps in the academy evidence analysis process. Publication bias was plotted by the use of a funnel plot with standard mean difference against standard error. Identified studies were meta-analyzed and stratified by body mass index, study design, dietary methodology, and country status (developed/developing) by the use of a random-effects model. Of 2487 articles screened, 18 studies met inclusion criteria. On average, women gained 12.0 (2.8) kg (standardized mean difference = 1.306, P < .0005) yet reported only a small increment in energy intake that did not reach statistical significance (∼475 kJ/day, standard mean difference = 0.266, P = .016). Irrespective of baseline body mass index, study design, dietary methodology, or country status, changes in energy intake were not significantly correlated to the amount of gestational weight gain (r = 0.321, P = .11). Despite rapid physiologic weight gain, women report little or no change in energy intake during pregnancy. Current recommendations to increase energy intake by ∼ 1000 kJ/day may, therefore, encourage excessive weight gain and adverse pregnancy outcomes. Copyright © 2016 Elsevier Inc. All rights reserved.

LigSearch: a knowledge-based web server to identify likely ligands for a protein target

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beer, Tjaart A. P. de; Laskowski, Roman A.; Duban, Mark-Eugene

LigSearch is a web server for identifying ligands likely to bind to a given protein. Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources. LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed. Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands. LigSearch can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch.

The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews.

PubMed

Bramer, Wichor M; Giustini, Dean; Kramer, Bianca Mr; Anderson, Pf

2013-12-23

The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs. The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database. GS' overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%. Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to optimize precision. Searches for SRs should be performed by experienced searchers creating searches that maximize recall for as many databases as deemed necessary by the search expert.

The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews

PubMed Central

2013-01-01

Background The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs. Methods The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database. Results GS’ overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%. Conclusions Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to optimize precision. Searches for SRs should be performed by experienced searchers creating searches that maximize recall for as many databases as deemed necessary by the search expert. PMID:24360284

Hospital nurses' information retrieval behaviours in relation to evidence based nursing: a literature review.

PubMed

Alving, Berit Elisabeth; Christensen, Janne Buck; Thrysøe, Lars

2018-03-01

The purpose of this literature review is to provide an overview of the information retrieval behaviour of clinical nurses, in terms of the use of databases and other information resources and their frequency of use. Systematic searches carried out in five databases and handsearching were used to identify the studies from 2010 to 2016, with a populations, exposures and outcomes (PEO) search strategy, focusing on the question: In which databases or other information resources do hospital nurses search for evidence based information, and how often? Of 5272 titles retrieved based on the search strategy, only nine studies fulfilled the criteria for inclusion. The studies are from the United States, Canada, Taiwan and Nigeria. The results show that hospital nurses' primary choice of source for evidence based information is Google and peers, while bibliographic databases such as PubMed are secondary choices. Data on frequency are only included in four of the studies, and data are heterogenous. The reasons for choosing Google and peers are primarily lack of time; lack of information; lack of retrieval skills; or lack of training in database searching. Only a few studies are published on clinical nurses' retrieval behaviours, and more studies are needed from Europe and Australia. © 2018 Health Libraries Group.

Influence of faith-based organisations on HIV prevention strategies in Africa: a systematic review.

PubMed

Ochillo, Marylyn A; van Teijlingen, Edwin; Hind, Martin

2017-09-01

The HIV/AIDS epidemic remains of global significance and there is a need to target sub-Saharan Africa since it is the hardest hit region worldwide. Religion and more specifically faith-based organisations can have an effect on socio-cultural factors that increase or decrease the risk of infection; and offer preventative interventions to the wider community. To understand the influence of faith-based organisations on HIV prevention in Africa. The main search engine of a British university 'mysearch' was used as this incorporates all relevant databases. Studies were also retrieved by searches within Google scholar, PubMed and reference lists of included papers were hand searched. The authors assessed the relevance of each article separately against the inclusion criteria. The data extraction form was piloted by the first author and cross-checked by the other authors. Seven studies met all inclusion criteria and were reviewed. Seven individual themes were identified. However, for the purposes of focus within this paper only two themes were focused on. Given the accessibility of faith-based organisations (FBOs) and the coverage of religion among the population, FBOs are potentially important players in HIV prevention. Therefore, more resources and support should be given to support their health promotion strategies.

Health-related quality of life measurement in women with polycystic ovary syndrome: a systematic review.

PubMed

Jones, G L; Hall, J M; Balen, A H; Ledger, W L

2008-01-01

The symptoms typically associated with polycystic ovary syndrome (PCOS) such as acne, hirsutism, irregular menses, amenorrhoea, obesity and subfertility are a major source of psychological morbidity and can negatively affect quality of life (QoL). We systematically searched the literature to identify the impact of symptoms and treatments for PCOS on health-related QoL (HRQoL) and to report on the types and psychometric properties of the instruments used. Papers were retrieved by systematically searching four electronic databases and hand searching relevant reference lists and bibliographies. Nineteen papers used a standardized questionnaire to measure health status; of these 12 (63.2%) used generic tools and 8 (42%) used the disease-specific PCOS questionnaire. Although a meta-analysis was not possible, it appears that weight concerns have a particular negative impact upon HRQoL, although the role of body mass index in affecting HRQoL scores is inconclusive from the available evidence. Acne is the area least reported upon in terms of its impact upon HRQoL. With the exception of three studies, most of the research has focused upon adult women with PCOS. Despite the benefits of HRQoL measures in research, few are being used to evaluate the outcomes of treatment for PCOS upon the subjective health status of women with the condition.

Gingival Retraction Methods: A Systematic Review.

PubMed

Tabassum, Sadia; Adnan, Samira; Khan, Farhan Raza

2017-12-01

The aim of this systematic review was to assess the gingival retraction methods in terms of the amount of gingival retraction achieved and changes observed in various clinical parameters: gingival index (GI), plaque index (PI), probing depth (PD), and attachment loss (AL). Data sources included three major databases, PubMed, CINAHL plus (Ebsco), and Cochrane, along with hand search. Search was made using the key terms in different permutations of gingival retraction* AND displacement method* OR technique* OR agents OR material* OR medicament*. The initial search results yielded 145 articles which were narrowed down to 10 articles using a strict eligibility criteria of including clinical trials or experimental studies on gingival retraction methods with the amount of tooth structure gained and assessment of clinical parameters as the outcomes conducted on human permanent teeth only. Gingival retraction was measured in 6/10 studies whereas the clinical parameters were assessed in 5/10 studies. The total number of teeth assessed in the 10 included studies was 400. The most common method used for gingival retraction was chemomechanical. The results were heterogeneous with regards to the outcome variables. No method seemed to be significantly superior to the other in terms of gingival retraction achieved. Clinical parameters were not significantly affected by the gingival retraction method. © 2016 by the American College of Prosthodontists.

Integrative Review of the Supportive Care Needs of Arab People Affected by Cancer

PubMed Central

Alananzeh, Ibrahim; Levesque, Janelle; Kwok, Cannas; Everett, Bronwyn

2016-01-01

This review aimed to identify the unmet supportive care needs to conduct an integrative review of the literature, to identify the unmet supportive care needs of Arab people affected by cancer (patients and caregivers), and the impact of these needs on quality of life and psychosocial well-being. In July 2015 databases, search engines and electronic list servers were searched, with no limit on the year of publication. Reference lists of included articles and published reviews were also hand searched. Six studies met the inclusion criteria. Most studies examined the supportive care/unmet needs of Arab cancer patients and their family caregivers. Language, communication, information, and the need to get relief from dependency were the most frequently reported unmet needs among Arab cancer patients. For immigrant Arab patients, physical unmet needs were higher than other migrant groups and native Anglo-Australians. Arab caregivers’ unmet needs included concerns about providing suitable care for their family member, sharing their experience with other caregivers, obtaining information, and, in the case of pediatric cancers, dealing with siblings’ emotional reactions. The existing literature exploring the unmet supportive care needs of Arab people affected by cancer is limited suggesting that comprehensive studies are needed to enhance our understanding of these needs and to inform service planning. PMID:27981153

Assessing the efficacy of different upper limb hemiparesis interventions on improving health-related quality of life in stroke patients: a systematic review.

PubMed

Pulman, Jennifer; Buckley, Emily

2013-01-01

This review aims to assess the efficacy of upper limb interventions on stroke survivors' health-related quality of life (QOL). Published studies were identified following a systematic search of the literature from 10 electronic databases, 3 subject-relevant journals, a Web search via a popular search engine, and reference lists of the included articles. In total, 22 articles met the inclusion criteria and were subjected to data extraction to establish the effectiveness of the intervention on QOL scores. Interventions varied according to their content, including acupuncture treatment, botulinum toxin type A (BTX-A) injections, constraint-induced movement therapy (CIMT), task training, and therapeutic exercise. Studies were required to have at least 1 quantitative outcome QOL measure. Of the 22 studies, 12 reported significant findings within groups and between control groups. Interventions including BTX-A injections, CIMT, exercise programs, baclofen pump, robotic-assisted therapy, electrical stimulation, and acupuncture were reported to significantly improve either overall health-related QOL or certain individual QOL domains, such as strength, hand function, memory, mood, activities of daily living, mobility, social participation, communication, energy, pain, and sleep. The review demonstrates the need for upper limb intervention studies to focus on QOL as a primary outcome measure in addition to the functional outcomes currently used.

Does Synergy Exist in Nursing? A Concept Analysis.

PubMed

Witges, Kim A; Scanlan, Judith M

2015-01-01

The aim is to analyze the concept of synergy, particularly as the concept applies to teamwork, and determine if the concept has utility in improving the work environment for nurses. Tackling nursing shortages that result from a poor work environment is a priority for many nurse leaders. Producing synergy among teams may be an effective strategy in enhancing the work environment. However, the understanding of synergy and the ability to produce synergy among teams has been seldom highlighted or discussed within nursing literature. Walker and Avant's approach was used to guide this concept analysis of synergy. Literature searches involved databases (PsycInfo, Medline, Cumulative Index for Nursing and Allied Health Literature [CINAHL], and Scopus), Internet search engines (Google), and hand searches. The analysis suggests that synergy is an outcome of the successful collaboration of the following three attributes: group cohesion, the pursuit of a common goal, and the achievement of a positive gain, considerably more than what was thought possible by the group. The foundation for this accomplishment requires an underlying feeling of special importance, the acknowledgment of each member's role, and open communication and dialogue among members. Nursing leaders would benefit from a broader understanding of synergy, and the mindful application and utility of synergy as an outcome of effective teamwork among nurses. © 2014 Wiley Periodicals, Inc.

Peer and family influence in eating disorders: a meta-analysis.

PubMed

Quiles Marcos, Y; Quiles Sebastián, M J; Pamies Aubalat, L; Botella Ausina, J; Treasure, J

2013-05-01

The aim of the present study was to undertake a systematic review using meta-analysis procedures to assess the relationships between eating disorders and peer and family influence and to evaluate whether gender plays a moderator role in that relationship. PsycINFO, Medline, Web of Science, EPSCO and Embase databases from 1980 to 2010 were searched in June and October 2010. Hand searching of relevant reference sections was also undertaken. It was possible to obtain 83 effect sizes from the 25 studies selected. Results showed that both peers and family influence dieting behavior, body dissatisfaction and bulimic symptoms in adolescent girls and boys. Furthermore, the analyses of the moderator variables showed that the variability of the effect sizes found was, in some cases, explained by gender, influence type and the country of the sample. These results highlight how daily social interactions can influence unhealthy eating practices in adolescent girls and boys, and suggest that weight-related issues of parents and peers can be transmitted to adolescents. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Widowhood and Mortality: A Meta-Analysis and Meta-Regressiona

PubMed Central

Roelfs, David J.; Shor, Eran; Curreli, Misty; Clemow, Lynn; Burg, Matthew M.; Schwartz, Joseph E.

2013-01-01

The study of spousal bereavement and mortality has long been a major topic of interest for social scientists, but much remains unknown with respect to important moderating factors such as age, follow-up duration, and geographic region. The present study examines these factors using meta-analysis. Keyword searches were conducted in multiple electronic databases, supplemented by extensive iterative hand searches. We extracted 1381 mortality risk estimates from 124 publications, providing data on more than 500 million persons. Compared to married people, widowers had a mean hazard ratio (HR) of 1.23 (95% confidence interval [CI], 1.19–1.28) among HRs adjusted for age and additional covariates and a high subjective quality score. The mean HR was higher for men (HR, 1.27; 95% CI, 1.19–1.35) than for women (HR, 1.15; 95% CI: 1.08–1.22). A significant interaction effect was found between gender and mean age, with HRs decreasing more rapidly for men than for women as age increased. Other significant predictors of HR magnitude included sample size, geographic region, level of statistical adjustment, and study quality. PMID:22427278

Faith-Based Institutions as Venues for Obesity Prevention.

PubMed

Maynard, Maria J

2017-06-01

The aim of this current narrative review is to critique the scope and value of recent studies with a focus on obesity-related health promotion in faith organizations. Electronic database searches, scanning of the reference lists of identified articles, and hand searching of journals for articles written in English and published in 2013-2016 revealed 16 studies. Half of the studies involved African-Americans, in churches and with predominantly female participants. Research among other ethnic groups was more likely to be exploratory. All of the 11 studies reporting the impact of programmes on weight-related measures showed favourable outcomes. However, due to study limitations (small sample size, short duration, attrition), significant unbiased effects cannot yet be concluded for most of the interventions reviewed. Study strengths included application of theory in community engagement and detailed description of cultural tailoring. Faith organizations show promise as settings for obesity prevention among high-risk groups, particularly African-Americans. Support for progressing formative work to adequately powered, randomized controlled trials is vital. Wider involvement of diverse faith settings and targeting obesity in men and childhood would be valuable developments.

Heath Beliefs of UK South Asians Related to Lifestyle Diseases: A Review of Qualitative Literature

PubMed Central

Lucas, Anna; Murray, Esther

2013-01-01

Objective. To review available qualitative evidence in the literature for health beliefs and perceptions specific to UK South Asian adults. Exploring available insight into the social and cultural constructs underlying perceptions related to health behaviours and lifestyle-related disease. Methods. A search of central databases and ethnic minority research groups was augmented by hand-searching of reference lists. For included studies, quality was assessed using a predetermined checklist followed by metaethnography to synthesise the findings, using both reciprocal translation and line-of-argument synthesis to look at factors impacting uptake of health behaviours. Results. A total of 10 papers varying in design and of good quality were included in the review. Cultural and social norms strongly influenced physical activity incidence and motivation as well as the ability to engage in healthy eating practices. Conclusions. These qualitative studies provide insight into approaches to health among UK South Asians in view of their social and cultural norms. Acknowledgement of their approach to lifestyle behaviours may assist acceptability of interventions and delivery of lifestyle advice by health professionals. PMID:23476751

Systematic Review of Breastfeeding and Herbs

PubMed Central

Budzynska, Katarzyna; Gardner, Zoë E.; Dugoua, Jean-Jacques; Low Dog, Tieraona

2012-01-01

Abstract Objectives Despite popular and historical use, there has been little modern research conducted to determine the safety and efficacy of herb use during breastfeeding. The purpose of this study was to systematically review the clinical literature on herbal medicine and lactation. Methods The databases PubMed, CAB Abstracts, Cochrane Central Register of Controlled Trials, HealthSTAR, Cumulative Index to Nursing and Allied Health Literature, and Reprotox were systematically searched for human trials from 1970 until 2010. Reference lists from relevant articles were hand-searched. Results Thirty-two studies met the inclusion criteria. Clinical studies were divided into three categories: survey studies (n=11), safety studies (n=8), and efficacy studies (n=13). Six studies were randomized controlled trials. The most common herbs studied were St. John's wort (Hypericum perforatum L.) (n=3), garlic (Allium sativum L.) extract (n=2), and senna (Cassia senna L.) (n=2). Studies were very heterogeneous with regard to study design, herbal intervention, and outcome measures. Overall, poor methodological quality predominated among the studies. Conclusions Our review concludes that further research is needed to assess the prevalence, efficacy, and safety of commonly used herbs during breastfeeding. PMID:22686865

Feminist conceptualizations of women's madness: a review of the literature.

PubMed

Wright, N; Owen, S

2001-10-01

Gender is one aspect of an individual's identity that has been widely debated and discussed in relation to many different aspects of social life. The literature review explores how gender stereotypes affect women and their experience of mental illness. The aim is to demonstrate how a feminist perspective provides a useful lens through which women's experience of mental illness can be viewed. The papers were identified by a computerized search of the CINAHL, Medline, BIDS ISI and Mental Health Nursing Collection databases and a hand search. All papers were screened and subjected to critical review. A theoretical framework was developed that reflected two key themes to emerge from the feminist literature on women and mental illness, namely psychiatry as a method of socially controlling women and the medicalization of women's unhappiness. In addition the complexities and contradictions in the feminist arguments are highlighted. The paper concludes by considering the implications of the issues raised for nursing practice by drawing attention to the current debates on the need to focus on gender relations rather than just on women's issues.

A Synthesis of Reading and Spelling Interventions and Their Effects on Spelling Outcomes for Students With Learning Disabilities

PubMed Central

Williams, Kelly J.; Walker, Melodee A.; Vaughn, Sharon; Wanzek, Jeanne

2016-01-01

Spelling is one of the most challenging areas for students with learning disabilities (LD), and improving spelling outcomes for these students is of high importance. In this synthesis, we examined the effects of spelling and reading interventions on spelling outcomes for students with LD in Grades K through 12. A systematic search of peer-reviewed literature published between 2004 and 2014 was conducted using electronic databases and hand searches of relevant journals. To be eligible for inclusion, studies had to meet the following criteria: (a) Participants were identified with LD and were in Grades K through 12, (b) designs were either treatment/comparison or single case, (c) a reading or spelling intervention was implemented, (d) at least one spelling outcome was measured, and (e) instruction was in English. Ten studies met criteria for inclusion in the synthesis, and effectiveness ranged from ineffective to highly effective. Findings demonstrated that spelling outcomes for taught words were improved for students with LD with the use of explicit instruction or self-correction strategies. PMID:26733209

A Synthesis of Reading and Spelling Interventions and Their Effects on Spelling Outcomes for Students With Learning Disabilities.

PubMed

Williams, Kelly J; Walker, Melodee A; Vaughn, Sharon; Wanzek, Jeanne

Spelling is one of the most challenging areas for students with learning disabilities (LD), and improving spelling outcomes for these students is of high importance. In this synthesis, we examined the effects of spelling and reading interventions on spelling outcomes for students with LD in Grades K through 12. A systematic search of peer-reviewed literature published between 2004 and 2014 was conducted using electronic databases and hand searches of relevant journals. To be eligible for inclusion, studies had to meet the following criteria: (a) Participants were identified with LD and were in Grades K through 12, (b) designs were either treatment/comparison or single case, (c) a reading or spelling intervention was implemented, (d) at least one spelling outcome was measured, and (e) instruction was in English. Ten studies met criteria for inclusion in the synthesis, and effectiveness ranged from ineffective to highly effective. Findings demonstrated that spelling outcomes for taught words were improved for students with LD with the use of explicit instruction or self-correction strategies.

Heath beliefs of UK South Asians related to lifestyle diseases: a review of qualitative literature.

PubMed

Lucas, Anna; Murray, Esther; Kinra, Sanjay

2013-01-01

To review available qualitative evidence in the literature for health beliefs and perceptions specific to UK South Asian adults. Exploring available insight into the social and cultural constructs underlying perceptions related to health behaviours and lifestyle-related disease. A search of central databases and ethnic minority research groups was augmented by hand-searching of reference lists. For included studies, quality was assessed using a predetermined checklist followed by metaethnography to synthesise the findings, using both reciprocal translation and line-of-argument synthesis to look at factors impacting uptake of health behaviours. A total of 10 papers varying in design and of good quality were included in the review. Cultural and social norms strongly influenced physical activity incidence and motivation as well as the ability to engage in healthy eating practices. These qualitative studies provide insight into approaches to health among UK South Asians in view of their social and cultural norms. Acknowledgement of their approach to lifestyle behaviours may assist acceptability of interventions and delivery of lifestyle advice by health professionals.

[The role of mobile communication devices in the spread of infections].

PubMed

Morvai, Júlia; Szabó, Rita

2015-05-17

Mobile communication devices have an invaluable feature of communication within hospital, and they may support certain aspects of clinical diagnosis and education. However, there may be a risk for contamination of these devices with various pathogens. The aim of the authors was to perform a systematic review on the potential role of mobile communication devices in the dissemination of pathogens and to identify effective prevention measures. A detailed literature search was conducted using PubMed and ScienceDirect databases for papers published in English between January, 2004 and August, 2014. With the use of specific search term combinations 30 of the 216 articles met the inclusion criteria. It was found that only 8% of healthcare workers routinely cleaned their mobile communication devices resulting in a high rate of contamination (40-100%). Coagulase-negative Staphylococci and Staphylococcus aureus were the most commonly identified bacteria and most of them were methicillin resistant (10-95.3%). This systematic review identified effective interventions to reduce bacterial contamination risks including staff education, hand hygiene and regular decontamination of mobile communication devices.

Brain-Derived Neurotrophic Factor Levels in Autism: A Systematic Review and Meta-Analysis.

PubMed

Saghazadeh, Amene; Rezaei, Nima

2017-04-01

Brain-derived neurotrophic factor (BDNF) plays an important role in activity-dependent synaptic plasticity. Altered blood BDNF levels have been frequently identified in people with autism spectrum disorders (ASD). There are however wide discrepancies in the evidence. Therefore, we performed the present systematic review and meta-analysis aimed at qualitative and quantitative synthesis of studies that measured blood BDNF levels in ASD and control subjects. Observational studies were identified through electronic database searching and also hand-searching of reference lists of relevant articles. A total of 183 papers were initially identified for review and eventually twenty studies were included in the meta-analysis. A meta-analysis of blood BDNF in 887 patients with ASD and 901 control subjects demonstrated significantly higher BDNF levels in ASD compared to controls with the SMD of 0.47 (95% CI 0.07-0.86, p = 0.02). In addition subgroup meta-analyses were performed based on the BDNF specimen. The present meta-analysis study led to conclusion that BDNF might play role in autism initiation/ propagation and therefore it can be considered as a possible biomarker of ASD.

Training and post-disaster interventions for the psychological impacts on disaster-exposed employees: a systematic review.

PubMed

Brooks, Samantha K; Dunn, Rebecca; Amlôt, Richard; Greenberg, Neil; Rubin, G James

2018-02-15

When organisations are exposed to traumatic situations, such as disasters, often staff are not prepared for the potential psychological impact which can negatively affect their wellbeing. To conduct a systematic review of the literature on psychological interventions aimed at improving staff wellbeing during or after disasters. Four electronic literature databases were searched. Reference lists of relevant articles were hand-searched. Fifteen articles were included. Five studies suggested that pre-disaster skills training and disaster education can improve employee confidence. Ten studies on post-disaster interventions revealed mixed findings on the effectiveness of psychological debriefing and limited evidence for cognitive behavioural therapy, psychoeducation and meditation. Pre-disaster training and education can improve employees' confidence in their ability to cope with disasters. The routine use of post-disaster psychological debriefings is not supported; further research is needed to determine if debriefing interventions could be useful in some circumstances. Further research is needed to provide more evidence on the potential positive effects of cognitive behavioural therapy, psychoeducation and meditation. More experimental studies on psychological disaster interventions are needed.

Optimization of the Controlled Evaluation of Closed Relational Queries

NASA Astrophysics Data System (ADS)

Biskup, Joachim; Lochner, Jan-Hendrik; Sonntag, Sebastian

For relational databases, controlled query evaluation is an effective inference control mechanism preserving confidentiality regarding a previously declared confidentiality policy. Implementations of controlled query evaluation usually lack efficiency due to costly theorem prover calls. Suitably constrained controlled query evaluation can be implemented efficiently, but is not flexible enough from the perspective of database users and security administrators. In this paper, we propose an optimized framework for controlled query evaluation in relational databases, being efficiently implementable on the one hand and relaxing the constraints of previous approaches on the other hand.

PlantGI: a database for searching gene indices in agricultural plants developed at NIAB, Korea

PubMed Central

Kim, Chang Kug; Choi, Ji Weon; Park, DongSuk; Kang, Man Jung; Seol, Young-Joo; Hyun, Do Yoon; Hahn, Jang Ho

2008-01-01

The Plant Gene Index (PlantGI) database is developed as a web-based search system with search capabilities for keywords to provide information on gene indices specifically for agricultural plants. The database contains specific Gene Index information for ten agricultural species, namely, rice, Chinese cabbage, wheat, maize, soybean, barley, mushroom, Arabidopsis, hot pepper and tomato. PlantGI differs from other Gene Index databases in being specific to agricultural plant species and thus complements services from similar other developments. The database includes options for interactive mining of EST CONTIGS and assembled EST data for user specific keyword queries. The current version of PlantGI contains a total of 34,000 EST CONTIGS data for rice (8488 records), wheat (8560 records), maize (4570 records), soybean (3726 records), barley (3417 records), Chinese cabbage (3602 records), tomato (1236 records), hot pepper (998 records), mushroom (130 records) and Arabidopsis (8 records). Availability The database is available for free at http://www.niab.go.kr/nabic/. PMID:18685722

Gallate Contact Dermatitis: Product Update and Systematic Review.

PubMed

Holcomb, Zachary E; Van Noord, Megan G; Atwater, Amber Reck

Allergic contact dermatitis related to cosmetic use can result from allergens not routinely evaluated by standard patch test protocols. Propyl, octyl, and dodecyl gallates are commonly used antioxidant preservatives with reports of associated allergic contact dermatitis in the literature. The objectives of this review were to investigate the role of gallates in allergic contact dermatitis and to explore products containing these preservatives. A systematic review of the literature through April 2016 was performed to explore cases of reported gallate allergy. Food and cosmetic product databases were searched for products containing gallates. Seventy-four cases of gallate contact allergy have been reported. In addition, a variety of commercially available cosmetic products and foods contain gallate chemicals. Propyl gallate is the most commonly reported gallate contact allergen and often causes facial and/or hand dermatitis.

Patient safety and infection control: bases for curricular integration.

PubMed

Silva, Andréa Mara Bernardes da; Bim, Lucas Lazarini; Bim, Felipe Lazarini; Sousa, Alvaro Francisco Lopes; Domingues, Pedro Castania Amadio; Nicolussi, Adriana Cristina; Andrade, Denise de

2018-05-01

To analyze curricular integration between teaching of patient safety and good infection prevention and control practices. Integrative review, designed to answer the question: "How does curricular integration of content about 'patient safety teaching' and content about 'infection prevention and control practices' occur in undergraduate courses in the health field?". The following databases were searched for primary studies: CINAHL, LILACS, ScienceDirect, Web of Science, Scopus, Europe PMC and MEDLINE. The final sample consisted of 13 studies. After content analysis, primary studies were grouped into two subject categories: "Innovative teaching practices" and "Curricular evaluation. Patient safety related to infection prevention and control practices is present in the curriculum of health undergraduate courses, but is not coordinated with other themes, is taught sporadically, and focuses mainly on hand hygiene.

Striving to live a normal life: a review of children and young people's experience of feeling different when living with a long term condition.

PubMed

Lambert, Veronica; Keogh, Deborah

2015-01-01

This paper presents a review of findings from qualitative studies on children's experience of feeling different when living with the long term conditions; diabetes, epilepsy and asthma. Following electronic database and hand searches of reference lists of identified papers, eighteen studies were selected for inclusion in the review. These studies revealed three common themes; participation in everyday life-restrictions and adjustments; treatment regimens-constraining and enabling; and communication-disclosure, stigma and support. Across these themes it was evident that children felt different physically and socially and they grappled constantly with balancing the dilemma of feeling and acting normal or feeling, being and revealing difference. Copyright © 2015 Elsevier Inc. All rights reserved.

Specialist Bibliographic Databases

PubMed Central

2016-01-01

Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls. PMID:27134485

Specialist Bibliographic Databases.

PubMed

Gasparyan, Armen Yuri; Yessirkepov, Marlen; Voronov, Alexander A; Trukhachev, Vladimir I; Kostyukova, Elena I; Gerasimov, Alexey N; Kitas, George D

2016-05-01

Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls.

Preconception risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease.

PubMed

Hussein, Norita; Weng, Stephen F; Kai, Joe; Kleijnen, Jos; Qureshi, Nadeem

2018-03-14

Globally, about five per cent of children are born with congenital or genetic disorders. The most common autosomal recessive conditions are thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease, with higher carrier rates in specific patient populations. Identifying and counselling couples at genetic risk of the conditions before pregnancy enables them to make fully informed reproductive decisions, with some of these choices not being available if genetic counselling is only offered in an antenatal setting. This is an update of a previously published review. To assess the effectiveness of systematic preconception genetic risk assessment to improve reproductive outcomes in women and their partners who are identified as carriers of thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease in healthcare settings when compared to usual care. We searched the Cochrane Cystic Fibrosis and Genetic Disorders Group's Trials Registers. In addition, we searched for all relevant trials from 1970 (or the date at which the database was first available if after 1970) to date using electronic databases (MEDLINE, Embase, CINAHL, PsycINFO), clinical trial databases (National Institutes of Health, Clinical Trials Search portal of the World Health Organization, metaRegister of controlled clinical trials), and hand searching of key journals and conference abstract books from 1998 to date (European Journal of Human Genetics, Genetics in Medicine, Journal of Community Genetics). We also searched the reference lists of relevant articles, reviews and guidelines and also contacted subject experts in the field to request any unpublished or other published trials.Date of latest search of the registers: 20 June 2017.Date of latest search of all other sources: 16 November 2017. Any randomised or quasi-randomised controlled trials (published or unpublished) comparing reproductive outcomes of systematic preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease when compared to usual care. We identified 25 papers, describing 16 unique trials which were potentially eligible for inclusion in the review. However, after assessment, no randomised controlled trials of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease were found. No randomised controlled trials of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis and Tay-Sachs disease were included. One ongoing trial has been identified which may potentially eligible for inclusion once completed. As no randomised controlled trials of preconception genetic risk assessment for thalassaemia, sickle cell disease, cystic fibrosis, or Tay-Sachs disease were found for inclusion in this review, the research evidence for current policy recommendations is limited to non-randomised studies.Information from well-designed, adequately powered, randomised trials is desirable in order to make more robust recommendations for practice. However, such trials must also consider the legal, ethical, and cultural barriers to implementation of preconception genetic risk assessment.

SinEx DB: a database for single exon coding sequences in mammalian genomes.

PubMed

Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S

2016-01-01

Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl. © The Author(s) 2016. Published by Oxford University Press.

Database Access Systems.

ERIC Educational Resources Information Center

Dalrymple, Prudence W.; Roderer, Nancy K.

1994-01-01

Highlights the changes that have occurred from 1987-93 in database access systems. Topics addressed include types of databases, including CD-ROMs; enduser interface; database selection; database access management, including library instruction and use of primary literature; economic issues; database users; the search process; and improving…

Front-End/Gateway Software: Availability and Usefulness.

ERIC Educational Resources Information Center

Kesselman, Martin

1985-01-01

Reviews features of front-end software packages (interface between user and online system)--database selection, search strategy development, saving and downloading, hardware and software requirements, training and documentation, online systems and database accession, and costs--and discusses gateway services (user searches through intermediary…

Digital Equipment Corporation's CRDOM Software and Database Publications.

ERIC Educational Resources Information Center

Adams, Michael Q.

1986-01-01

Acquaints information professionals with Digital Equipment Corporation's compact optical disk read-only-memory (CDROM) search and retrieval software and growing library of CDROM database publications (COMPENDEX, Chemical Abstracts Services). Highlights include MicroBASIS, boolean operators, range operators, word and phrase searching, proximity…

Competitive code-based fast palmprint identification using a set of cover trees

NASA Astrophysics Data System (ADS)

Yue, Feng; Zuo, Wangmeng; Zhang, David; Wang, Kuanquan

2009-06-01

A palmprint identification system recognizes a query palmprint image by searching for its nearest neighbor from among all the templates in a database. When applied on a large-scale identification system, it is often necessary to speed up the nearest-neighbor searching process. We use competitive code, which has very fast feature extraction and matching speed, for palmprint identification. To speed up the identification process, we extend the cover tree method and propose to use a set of cover trees to facilitate the fast and accurate nearest-neighbor searching. We can use the cover tree method because, as we show, the angular distance used in competitive code can be decomposed into a set of metrics. Using the Hong Kong PolyU palmprint database (version 2) and a large-scale palmprint database, our experimental results show that the proposed method searches for nearest neighbors faster than brute force searching.

MEDLINE versus EMBASE and CINAHL for telemedicine searches.

PubMed

Bahaadinbeigy, Kambiz; Yogesan, Kanagasingam; Wootton, Richard

2010-10-01

Researchers in the domain of telemedicine throughout the world tend to search multiple bibliographic databases to retrieve the highest possible number of publications when conducting review projects. Medical Literature Analysis and Retrieval System Online (MEDLINE), Excerpta Medica Database (EMBASE), and Cumulative Index to Nursing and Allied Health Literature (CINAHL) are three popular databases in the discipline of biomedicine that are used for conducting reviews. Access to the MEDLINE database is free and easy, whereas EMBASE and CINAHL are not free and sometimes not easy to access for researchers in small research centers. This project sought to compare MEDLINE with EMBASE and CINAHL to estimate what proportion of potentially relevant publications would be missed when only MEDLINE is used in a review project, in comparison to when EMBASE and CINAHL are also used. Twelve simple keywords relevant to 12 different telemedicine applications were searched using all three databases, and the results were compared. About 9%-18% of potentially relevant articles would have been missed if MEDLINE had been the only database used. It is preferable if all three or more databases are used when conducting a review in telemedicine. Researchers from developing countries or small research institutions could rely on only MEDLINE, but they would loose 9%-18% of the potentially relevant publications. Searching MEDLINE alone is not ideal, but in a resource-constrained situation, it is definitely better than nothing.

Improvements to the Magnetics Information Consortium (MagIC) Paleo and Rock Magnetic Database

NASA Astrophysics Data System (ADS)

Jarboe, N.; Minnett, R.; Tauxe, L.; Koppers, A. A. P.; Constable, C.; Jonestrask, L.

2015-12-01

The Magnetic Information Consortium (MagIC) database (http://earthref.org/MagIC/) continues to improve the ease of data uploading and editing, the creation of complex searches, data visualization, and data downloads for the paleomagnetic, geomagnetic, and rock magnetic communities. Online data editing is now available and the need for proprietary spreadsheet software is therefore entirely negated. The data owner can change values in the database or delete entries through an HTML 5 web interface that resembles typical spreadsheets in behavior and uses. Additive uploading now allows for additions to data sets to be uploaded with a simple drag and drop interface. Searching the database has improved with the addition of more sophisticated search parameters and with the facility to use them in complex combinations. A comprehensive summary view of a search result has been added for increased quick data comprehension while a raw data view is available if one desires to see all data columns as stored in the database. Data visualization plots (ARAI, equal area, demagnetization, Zijderveld, etc.) are presented with the data when appropriate to aid the user in understanding the dataset. MagIC data associated with individual contributions or from online searches may be downloaded in the tab delimited MagIC text file format for susbsequent offline use and analysis. With input from the paleomagnetic, geomagnetic, and rock magnetic communities, the MagIC database will continue to improve as a data warehouse and resource.

An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values.

PubMed

Sakurai, Nozomu; Ara, Takeshi; Kanaya, Shigehiko; Nakamura, Yukiko; Iijima, Yoko; Enomoto, Mitsuo; Motegi, Takeshi; Aoki, Koh; Suzuki, Hideyuki; Shibata, Daisuke

2013-01-15

High-accuracy mass values detected by high-resolution mass spectrometry analysis enable prediction of elemental compositions, and thus are used for metabolite annotations in metabolomic studies. Here, we report an application of a relational database to significantly improve the rate of elemental composition predictions. By searching a database of pre-calculated elemental compositions with fixed kinds and numbers of atoms, the approach eliminates redundant evaluations of the same formula that occur in repeated calculations with other tools. When our approach is compared with HR2, which is one of the fastest tools available, our database search times were at least 109 times shorter than those of HR2. When a solid-state drive (SSD) was applied, the search time was 488 times shorter at 5 ppm mass tolerance and 1833 times at 0.1 ppm. Even if the search by HR2 was performed with 8 threads in a high-spec Windows 7 PC, the database search times were at least 26 and 115 times shorter without and with the SSD. These improvements were enhanced in a low spec Windows XP PC. We constructed a web service 'MFSearcher' to query the database in a RESTful manner. Available for free at http://webs2.kazusa.or.jp/mfsearcher. The web service is implemented in Java, MySQL, Apache and Tomcat, with all major browsers supported. sakurai@kazusa.or.jp Supplementary data are available at Bioinformatics online.

Data-driven grasp synthesis using shape matching and task-based pruning.

PubMed

Li, Ying; Fu, Jiaxin L; Pollard, Nancy S

2007-01-01

Human grasps, especially whole-hand grasps, are difficult to animate because of the high number of degrees of freedom of the hand and the need for the hand to conform naturally to the object surface. Captured human motion data provides us with a rich source of examples of natural grasps. However, for each new object, we are faced with the problem of selecting the best grasp from the database and adapting it to that object. This paper presents a data-driven approach to grasp synthesis. We begin with a database of captured human grasps. To identify candidate grasps for a new object, we introduce a novel shape matching algorithm that matches hand shape to object shape by identifying collections of features having similar relative placements and surface normals. This step returns many grasp candidates, which are clustered and pruned by choosing the grasp best suited for the intended task. For pruning undesirable grasps, we develop an anatomically-based grasp quality measure specific to the human hand. Examples of grasp synthesis are shown for a variety of objects not present in the original database. This algorithm should be useful both as an animator tool for posing the hand and for automatic grasp synthesis in virtual environments.

Introducing a New Interface for the Online MagIC Database by Integrating Data Uploading, Searching, and Visualization

NASA Astrophysics Data System (ADS)

Jarboe, N.; Minnett, R.; Constable, C.; Koppers, A. A.; Tauxe, L.

2013-12-01

The Magnetics Information Consortium (MagIC) is dedicated to supporting the paleomagnetic, geomagnetic, and rock magnetic communities through the development and maintenance of an online database (http://earthref.org/MAGIC/), data upload and quality control, searches, data downloads, and visualization tools. While MagIC has completed importing some of the IAGA paleomagnetic databases (TRANS, PINT, PSVRL, GPMDB) and continues to import others (ARCHEO, MAGST and SECVR), further individual data uploading from the community contributes a wealth of easily-accessible rich datasets. Previously uploading of data to the MagIC database required the use of an Excel spreadsheet using either a Mac or PC. The new method of uploading data utilizes an HTML 5 web interface where the only computer requirement is a modern browser. This web interface will highlight all errors discovered in the dataset at once instead of the iterative error checking process found in the previous Excel spreadsheet data checker. As a web service, the community will always have easy access to the most up-to-date and bug free version of the data upload software. The filtering search mechanism of the MagIC database has been changed to a more intuitive system where the data from each contribution is displayed in tables similar to how the data is uploaded (http://earthref.org/MAGIC/search/). Searches themselves can be saved as a permanent URL, if desired. The saved search URL could then be used as a citation in a publication. When appropriate, plots (equal area, Zijderveld, ARAI, demagnetization, etc.) are associated with the data to give the user a quicker understanding of the underlying dataset. The MagIC database will continue to evolve to meet the needs of the paleomagnetic, geomagnetic, and rock magnetic communities.

CHERNOLITTM. Chernobyl Bibliographic Search System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caff, F., Jr.; Kennedy, R.A.; Mahaffey, J.A.

1992-03-02

The Chernobyl Bibliographic Search System (Chernolit TM) provides bibliographic data in a usable format for research studies relating to the Chernobyl nuclear accident that occurred in the former Ukrainian Republic of the USSR in 1986. Chernolit TM is a portable and easy to use product. The bibliographic data is provided under the control of a graphical user interface so that the user may quickly and easily retrieve pertinent information from the large database. The user may search the database for occurrences of words, names, or phrases; view bibliographic references on screen; and obtain reports of selected references. Reports may bemore » viewed on the screen, printed, or accumulated in a folder that is written to a disk file when the user exits the software. Chernolit TM provides a cost-effective alternative to multiple, independent literature searches. Forty-five hundred references concerning the accident, including abstracts, are distributed with Chernolit TM. The data contained in the database were obtained from electronic literature searches and from requested donations from individuals and organizations. These literature searches interrogated the Energy Science and Technology database (formerly DOE ENERGY) of the DIALOG Information Retrieval Service. Energy Science and Technology, provided by the U.S. DOE, Washington, D.C., is a multi-disciplinary database containing references to the world`s scientific and technical literature on energy. All unclassified information processed at the Office of Scientific and Technical Information (OSTI) of the U.S. DOE is included in the database. In addition, information on many documents has been manually added to Chernolit TM. Most of this information was obtained in response to requests for data sent to people and/or organizations throughout the world.« less

Chernobyl Bibliographic Search System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carr, Jr, F.; Kennedy, R. A.; Mahaffey, J. A.

1992-05-11

The Chernobyl Bibliographic Search System (Chernolit TM) provides bibliographic data in a usable format for research studies relating to the Chernobyl nuclear accident that occurred in the former Ukrainian Republic of the USSR in 1986. Chernolit TM is a portable and easy to use product. The bibliographic data is provided under the control of a graphical user interface so that the user may quickly and easily retrieve pertinent information from the large database. The user may search the database for occurrences of words, names, or phrases; view bibliographic references on screen; and obtain reports of selected references. Reports may bemore » viewed on the screen, printed, or accumulated in a folder that is written to a disk file when the user exits the software. Chernolit TM provides a cost-effective alternative to multiple, independent literature searches. Forty-five hundred references concerning the accident, including abstracts, are distributed with Chernolit TM. The data contained in the database were obtained from electronic literature searches and from requested donations from individuals and organizations. These literature searches interrogated the Energy Science and Technology database (formerly DOE ENERGY) of the DIALOG Information Retrieval Service. Energy Science and Technology, provided by the U.S. DOE, Washington, D.C., is a multi-disciplinary database containing references to the world''s scientific and technical literature on energy. All unclassified information processed at the Office of Scientific and Technical Information (OSTI) of the U.S. DOE is included in the database. In addition, information on many documents has been manually added to Chernolit TM. Most of this information was obtained in response to requests for data sent to people and/or organizations throughout the world.« less

NASA Image eXchange (NIX)

NASA Technical Reports Server (NTRS)

vonOfenheim. William H. C.; Heimerl, N. Lynn; Binkley, Robert L.; Curry, Marty A.; Slater, Richard T.; Nolan, Gerald J.; Griswold, T. Britt; Kovach, Robert D.; Corbin, Barney H.; Hewitt, Raymond W.

1998-01-01

This paper discusses the technical aspects of and the project background for the NASA Image exchange (NIX). NIX, which provides a single entry point to search selected image databases at the NASA Centers, is a meta-search engine (i.e., a search engine that communicates with other search engines). It uses these distributed digital image databases to access photographs, animations, and their associated descriptive information (meta-data). NIX is available for use at the following URL: http://nix.nasa.gov./NIX, which was sponsored by NASAs Scientific and Technical Information (STI) Program, currently serves images from seven NASA Centers. Plans are under way to link image databases from three additional NASA Centers. images and their associated meta-data, which are accessible by NIX, reside at the originating Centers, and NIX utilizes a virtual central site that communicates with each of these sites. Incorporated into the virtual central site are several protocols to support searches from a diverse collection of database engines. The searches are performed in parallel to ensure optimization of response times. To augment the search capability, browse functionality with pre-defined categories has been built into NIX, thereby ensuring dissemination of 'best-of-breed' imagery. As a final recourse, NIX offers access to a help desk via an on-line form to help locate images and information either within the scope of NIX or from available external sources.

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2011 CFR

2011-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2010 CFR

2010-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2014 CFR

2014-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2012 CFR

2012-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

49 CFR 1572.107 - Other analyses.

Code of Federal Regulations, 2013 CFR

2013-10-01

... applicant poses a security threat based on a search of the following databases: (1) Interpol and other international databases, as appropriate. (2) Terrorist watchlists and related databases. (3) Any other databases...

Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture.

PubMed

Azman, Syafiq Kamarul; Anwar, Muhammad Zohaib; Henschel, Andreas

2017-07-24

Given the current influx of 16S rRNA profiles of microbiota samples, it is conceivable that large amounts of them eventually are available for search, comparison and contextualization with respect to novel samples. This process facilitates the identification of similar compositional features in microbiota elsewhere and therefore can help to understand driving factors for microbial community assembly. We present Visibiome, a microbiome search engine that can perform exhaustive, phylogeny based similarity search and contextualization of user-provided samples against a comprehensive dataset of 16S rRNA profiles environments, while tackling several computational challenges. In order to scale to high demands, we developed a distributed system that combines web framework technology, task queueing and scheduling, cloud computing and a dedicated database server. To further ensure speed and efficiency, we have deployed Nearest Neighbor search algorithms, capable of sublinear searches in high-dimensional metric spaces in combination with an optimized Earth Mover Distance based implementation of weighted UniFrac. The search also incorporates pairwise (adaptive) rarefaction and optionally, 16S rRNA copy number correction. The result of a query microbiome sample is the contextualization against a comprehensive database of microbiome samples from a diverse range of environments, visualized through a rich set of interactive figures and diagrams, including barchart-based compositional comparisons and ranking of the closest matches in the database. Visibiome is a convenient, scalable and efficient framework to search microbiomes against a comprehensive database of environmental samples. The search engine leverages a popular but computationally expensive, phylogeny based distance metric, while providing numerous advantages over the current state of the art tool.

The Relationship between Searches Performed in Online Databases and the Number of Full-Text Articles Accessed: Measuring the Interaction between Database and E-Journal Collections

ERIC Educational Resources Information Center

Lamothe, Alain R.

2011-01-01

The purpose of this paper is to report the results of a quantitative analysis exploring the interaction and relationship between the online database and electronic journal collections at the J. N. Desmarais Library of Laurentian University. A very strong relationship exists between the number of searches and the size of the online database…

Decision making in family medicine

PubMed Central

Labrecque, Michel; Ratté, Stéphane; Frémont, Pierre; Cauchon, Michel; Ouellet, Jérôme; Hogg, William; McGowan, Jessie; Gagnon, Marie-Pierre; Njoya, Merlin; Légaré, France

2013-01-01

Abstract Objective To compare the ability of users of 2 medical search engines, InfoClinique and the Trip database, to provide correct answers to clinical questions and to explore the perceived effects of the tools on the clinical decision-making process. Design Randomized trial. Setting Three family medicine units of the family medicine program of the Faculty of Medicine at Laval University in Quebec city, Que. Participants Fifteen second-year family medicine residents. Intervention Residents generated 30 structured questions about therapy or preventive treatment (2 questions per resident) based on clinical encounters. Using an Internet platform designed for the trial, each resident answered 20 of these questions (their own 2, plus 18 of the questions formulated by other residents, selected randomly) before and after searching for information with 1 of the 2 search engines. For each question, 5 residents were randomly assigned to begin their search with InfoClinique and 5 with the Trip database. Main outcome measures The ability of residents to provide correct answers to clinical questions using the search engines, as determined by third-party evaluation. After answering each question, participants completed a questionnaire to assess their perception of the engine’s effect on the decision-making process in clinical practice. Results Of 300 possible pairs of answers (1 answer before and 1 after the initial search), 254 (85%) were produced by 14 residents. Of these, 132 (52%) and 122 (48%) pairs of answers concerned questions that had been assigned an initial search with InfoClinique and the Trip database, respectively. Both engines produced an important and similar absolute increase in the proportion of correct answers after searching (26% to 62% for InfoClinique, for an increase of 36%; 24% to 63% for the Trip database, for an increase of 39%; P = .68). For all 30 clinical questions, at least 1 resident produced the correct answer after searching with either search engine. The mean (SD) time of the initial search for each question was 23.5 (7.6) minutes with InfoClinique and 22.3 (7.8) minutes with the Trip database (P = .30). Participants’ perceptions of each engine’s effect on the decision-making process were very positive and similar for both search engines. Conclusion Family medicine residents’ ability to provide correct answers to clinical questions increased dramatically and similarly with the use of both InfoClinique and the Trip database. These tools have strong potential to increase the quality of medical care. PMID:24130286

High School Students, Libraries, and the Search Process. An Analysis of Student Materials and Facilities Usage Patterns in Delaware Following Introduction of Online Bibliographic Database Searching.

ERIC Educational Resources Information Center

Mancall, Jacqueline C.; Deskins, Dreama

This report assesses the impact of instruction in online bibliographic database searching on high school students' use of library materials and facilities in three Delaware secondary schools (one public, one parochial, and one private) during the spring of 1984. Most students involved in the analysis were given a brief explanation of online…

Strategies for discontinuation of proton pump inhibitors: a systematic review.

PubMed

Haastrup, Peter; Paulsen, Maja S; Begtrup, Luise M; Hansen, Jane M; Jarbøl, Dorte E

2014-12-01

Proton pump inhibitors (PPIs) are considered to be overprescribed. Consensus on how to attempt discontinuation is, however, lacking. We therefore conducted a systematic review of clinical studies on discontinuation of PPIs. Systematic review based on clinical studies investigating discontinuation strategies and discontinuation rates for users of antisecretory medication judged eligible for withdrawal. The databases Medline, Embase and Cochrane Library were searched to December 2013 using the terms antisecretory, anti-ulcer, PPI, acid suppressant, discontinuation, step-down, step down, cessation, tapering, withdrawal and withhold. Search terms were used either singularly or in combination. Papers written in English or Scandinavian were included. Concurrent hand searching was undertaken to pursue references of references. The website ClinicalTrials.gov was searched for unpublished results and ongoing studies. A total of 371 abstracts were scrutinized to determine relevancy. The thorough search resulted in six clinical studies on strategies for discontinuation of PPIs. All discontinuation regimens used in the studies differed, and several interventions have been tested in order to decrease use of PPIs. Discontinuations were reported across all studies ranging from 14% to 64% without deteriorating symptom control. Tapering seems to be a more effective discontinuation strategy than abrupt discontinuation. Discontinuation of PPIs is feasible in a clinical setting, and a substantial number of the patients treated without a clear indication can safely reduce or discontinue treatment. Tapering seems to be the most effective way of doing this. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System.

PubMed

Liu, Yu; Hong, Yang; Lin, Chun-Yuan; Hung, Che-Lun

2015-01-01

The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS) to eliminate the unnecessary alignments. The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively.

A Bayesian network approach to the database search problem in criminal proceedings

PubMed Central

2012-01-01

Background The ‘database search problem’, that is, the strengthening of a case - in terms of probative value - against an individual who is found as a result of a database search, has been approached during the last two decades with substantial mathematical analyses, accompanied by lively debate and centrally opposing conclusions. This represents a challenging obstacle in teaching but also hinders a balanced and coherent discussion of the topic within the wider scientific and legal community. This paper revisits and tracks the associated mathematical analyses in terms of Bayesian networks. Their derivation and discussion for capturing probabilistic arguments that explain the database search problem are outlined in detail. The resulting Bayesian networks offer a distinct view on the main debated issues, along with further clarity. Methods As a general framework for representing and analyzing formal arguments in probabilistic reasoning about uncertain target propositions (that is, whether or not a given individual is the source of a crime stain), this paper relies on graphical probability models, in particular, Bayesian networks. This graphical probability modeling approach is used to capture, within a single model, a series of key variables, such as the number of individuals in a database, the size of the population of potential crime stain sources, and the rarity of the corresponding analytical characteristics in a relevant population. Results This paper demonstrates the feasibility of deriving Bayesian network structures for analyzing, representing, and tracking the database search problem. The output of the proposed models can be shown to agree with existing but exclusively formulaic approaches. Conclusions The proposed Bayesian networks allow one to capture and analyze the currently most well-supported but reputedly counter-intuitive and difficult solution to the database search problem in a way that goes beyond the traditional, purely formulaic expressions. The method’s graphical environment, along with its computational and probabilistic architectures, represents a rich package that offers analysts and discussants with additional modes of interaction, concise representation, and coherent communication. PMID:22849390

[International bibliographic databases--Current Contents on disk and in FTP format (Internet): presentation and guide].

PubMed

Bloch-Mouillet, E

1999-01-01

This paper aims to provide technical and practical advice about finding references using Current Contents on disk (Macintosh or PC) or via the Internet (FTP). Seven editions are published each week. They are all organized in the same way and have the same search engine. The Life Sciences edition, extensively used in medical research, is presented here in detail, as an example. This methodological note explains, in French, how to use this reference database. It is designed to be a practical guide for browsing and searching the database, and particularly for creating search profiles adapted to the needs of researchers.

Electromyography data for non-invasive naturally-controlled robotic hand prostheses

PubMed Central

Atzori, Manfredo; Gijsberts, Arjan; Castellini, Claudio; Caputo, Barbara; Hager, Anne-Gabrielle Mittaz; Elsig, Simone; Giatsidis, Giorgio; Bassetto, Franco; Müller, Henning

2014-01-01

Recent advances in rehabilitation robotics suggest that it may be possible for hand-amputated subjects to recover at least a significant part of the lost hand functionality. The control of robotic prosthetic hands using non-invasive techniques is still a challenge in real life: myoelectric prostheses give limited control capabilities, the control is often unnatural and must be learned through long training times. Meanwhile, scientific literature results are promising but they are still far from fulfilling real-life needs. This work aims to close this gap by allowing worldwide research groups to develop and test movement recognition and force control algorithms on a benchmark scientific database. The database is targeted at studying the relationship between surface electromyography, hand kinematics and hand forces, with the final goal of developing non-invasive, naturally controlled, robotic hand prostheses. The validation section verifies that the data are similar to data acquired in real-life conditions, and that recognition of different hand tasks by applying state-of-the-art signal features and machine-learning algorithms is possible. PMID:25977804

Search for anomalous top-quark couplings with the D0 detector.

PubMed

Abazov, V M; Abbott, B; Abolins, M; Acharya, B S; Adams, M; Adams, T; Aguilo, E; Ahsan, M; Alexeev, G D; Alkhazov, G; Alton, A; Alverson, G; Alves, G A; Anastasoaie, M; Ancu, L S; Andeen, T; Andrieu, B; Anzelc, M S; Aoki, M; Arnoud, Y; Arov, M; Arthaud, M; Askew, A; Asman, B; Assis Jesus, A C S; Atramentov, O; Avila, C; Backusmayes, J; Badaud, F; Bagby, L; Baldin, B; Bandurin, D V; Banerjee, P; Banerjee, S; Barberis, E; Barfuss, A-F; Bargassa, P; Baringer, P; Barreto, J; Bartlett, J F; Bassler, U; Bauer, D; Beale, S; Bean, A; Begalli, M; Begel, M; Belanger-Champagne, C; Bellantoni, L; Bellavance, A; Benitez, J A; Beri, S B; Bernardi, G; Bernhard, R; Bertram, I; Besançon, M; Beuselinck, R; Bezzubov, V A; Bhat, P C; Bhatnagar, V; Blazey, G; Blekman, F; Blessing, S; Bloom, K; Boehnlein, A; Boline, D; Bolton, T A; Boos, E E; Borissov, G; Bose, T; Brandt, A; Brock, R; Brooijmans, G; Bross, A; Brown, D; Bu, X B; Buchanan, N J; Buchholz, D; Buehler, M; Buescher, V; Bunichev, V; Burdin, S; Burnett, T H; Buszello, C P; Calfayan, P; Calpas, B; Calvet, S; Cammin, J; Carrasco-Lizarraga, M A; Carrera, E; Carvalho, W; Casey, B C K; Castilla-Valdez, H; Chakrabarti, S; Chakraborty, D; Chan, K M; Chandra, A; Cheu, E; Cho, D K; Choi, S; Choudhary, B; Christofek, L; Christoudias, T; Cihangir, S; Claes, D; Clutter, J; Cooke, M; Cooper, W E; Corcoran, M; Couderc, F; Cousinou, M-C; Crépé-Renaudin, S; Cuplov, V; Cutts, D; Cwiok, M; da Motta, H; Das, A; Davies, G; De, K; de Jong, S J; De La Cruz-Burelo, E; De Oliveira Martins, C; DeVaughan, K; Déliot, F; Demarteau, M; Demina, R; Denisov, D; Denisov, S P; Desai, S; Diehl, H T; Diesburg, M; Dominguez, A; Dorland, T; Dubey, A; Dudko, L V; Duflot, L; Dugad, S R; Duggan, D; Duperrin, A; Dutt, S; Dyer, J; Dyshkant, A; Eads, M; Edmunds, D; Ellison, J; Elvira, V D; Enari, Y; Eno, S; Ermolov, P; Escalier, M; Evans, H; Evdokimov, A; Evdokimov, V N; Ferapontov, A V; Ferbel, T; Fiedler, F; Filthaut, F; Fisher, W; Fisk, H E; Fortner, M; Fox, H; Fu, S; Fuess, S; Gadfort, T; Galea, C F; Garcia, C; Garcia-Bellido, A; Gavrilov, V; Gay, P; Geist, W; Geng, W; Gerber, C E; Gershtein, Y; Gillberg, D; Ginther, G; Gómez, B; Goussiou, A; Grannis, P D; Greenlee, H; Greenwood, Z D; Gregores, E M; Grenier, G; Gris, Ph; Grivaz, J-F; Grohsjean, A; Grünendahl, S; Grünewald, M W; Guo, F; Guo, J; Gutierrez, G; Gutierrez, P; Haas, A; Hadley, N J; Haefner, P; Hagopian, S; Haley, J; Hall, I; Hall, R E; Han, L; Harder, K; Harel, A; Hauptman, J M; Hays, J; Hebbeker, T; Hedin, D; Hegeman, J G; Heinson, A P; Heintz, U; Hensel, C; Herner, K; Hesketh, G; Hildreth, M D; Hirosky, R; Hoang, T; Hobbs, J D; Hoeneisen, B; Hohlfeld, M; Hossain, S; Houben, P; Hu, Y; Hubacek, Z; Huske, N; Hynek, V; Iashvili, I; Illingworth, R; Ito, A S; Jabeen, S; Jaffré, M; Jain, S; Jakobs, K; Jarvis, C; Jesik, R; Johns, K; Johnson, C; Johnson, M; Johnston, D; Jonckheere, A; Jonsson, P; Juste, A; Kajfasz, E; Karmanov, D; Kasper, P A; Katsanos, I; Kaushik, V; Kehoe, R; Kermiche, S; Khalatyan, N; Khanov, A; Kharchilava, A; Kharzheev, Y N; Khatidze, D; Kim, T J; Kirby, M H; Kirsch, M; Klima, B; Kohli, J M; Konrath, J-P; Kozelov, A V; Kraus, J; Kuhl, T; Kumar, A; Kupco, A; Kurca, T; Kuzmin, V A; Kvita, J; Lacroix, F; Lam, D; Lammers, S; Landsberg, G; Lebrun, P; Lee, W M; Leflat, A; Lellouch, J; Li, J; Li, L; Li, Q Z; Lietti, S M; Lim, J K; Lima, J G R; Lincoln, D; Linnemann, J; Lipaev, V V; Lipton, R; Liu, Y; Liu, Z; Lobodenko, A; Lokajicek, M; Love, P; Lubatti, H J; Luna-Garcia, R; Lyon, A L; Maciel, A K A; Mackin, D; Madaras, R J; Mättig, P; Magerkurth, A; Mal, P K; Malbouisson, H B; Malik, S; Malyshev, V L; Maravin, Y; Martin, B; McCarthy, R; Meijer, M M; Melnitchouk, A; Mendoza, L; Mercadante, P G; Merkin, M; Merritt, K W; Meyer, A; Meyer, J; Mitrevski, J; Mommsen, R K; Mondal, N K; Moore, R W; Moulik, T; Muanza, G S; Mulhearn, M; Mundal, O; Mundim, L; Nagy, E; Naimuddin, M; Narain, M; Neal, H A; Negret, J P; Neustroev, P; Nilsen, H; Nogima, H; Novaes, S F; Nunnemann, T; O'Neil, D C; Obrant, G; Ochando, C; Onoprienko, D; Oshima, N; Osman, N; Osta, J; Otec, R; Otero y Garzón, G J; Owen, M; Padilla, M; Padley, P; Pangilinan, M; Parashar, N; Park, S-J; Park, S K; Parsons, J; Partridge, R; Parua, N; Patwa, A; Pawloski, G; Penning, B; Perfilov, M; Peters, K; Peters, Y; Pétroff, P; Petteni, M; Piegaia, R; Piper, J; Pleier, M-A; Podesta-Lerma, P L M; Podstavkov, V M; Pogorelov, Y; Pol, M-E; Polozov, P; Pope, B G; Popov, A V; Potter, C; da Silva, W L Prado; Prosper, H B; Protopopescu, S; Qian, J; Quadt, A; Quinn, B; Rakitine, A; Rangel, M S; Ranjan, K; Ratoff, P N; Renkel, P; Rich, P; Rijssenbeek, M; Ripp-Baudot, I; Rizatdinova, F; Robinson, S; Rodrigues, R F; Rominsky, M; Royon, C; Rubinov, P; Ruchti, R; Safronov, G; Sajot, G; Sánchez-Hernández, A; Sanders, M P; Sanghi, B; Savage, G; Sawyer, L; Scanlon, T; Schaile, D; Schamberger, R D; Scheglov, Y; Schellman, H; Schliephake, T; Schlobohm, S; Schwanenberger, C; Schwienhorst, R; Sekaric, J; Severini, H; Shabalina, E; Shamim, M; Shary, V; Shchukin, A A; Shivpuri, R K; Siccardi, V; Simak, V; Sirotenko, V; Skubic, P; Slattery, P; Smirnov, D; Snow, G R; Snow, J; Snyder, S; Söldner-Rembold, S; Sonnenschein, L; Sopczak, A; Sosebee, M; Soustruznik, K; Spurlock, B; Stark, J; Stolin, V; Stoyanova, D A; Strandberg, J; Strandberg, S; Strang, M A; Strauss, E; Strauss, M; Ströhmer, R; Strom, D; Stutte, L; Sumowidagdo, S; Svoisky, P; Sznajder, A; Tanasijczuk, A; Taylor, W; Tiller, B; Tissandier, F; Titov, M; Tokmenin, V V; Torchiani, I; Tsybychev, D; Tuchming, B; Tully, C; Tuts, P M; Unalan, R; Uvarov, L; Uvarov, S; Uzunyan, S; Vachon, B; van den Berg, P J; Van Kooten, R; van Leeuwen, W M; Varelas, N; Varnes, E W; Vasilyev, I A; Verdier, P; Vertogradov, L S; Verzocchi, M; Vilanova, D; Villeneuve-Seguier, F; Vint, P; Vokac, P; Voutilainen, M; Wagner, R; Wahl, H D; Wang, M H L S; Warchol, J; Watts, G; Wayne, M; Weber, G; Weber, M; Welty-Rieger, L; Wenger, A; Wermes, N; Wetstein, M; White, A; Wicke, D; Williams, M R J; Wilson, G W; Wimpenny, S J; Wobisch, M; Wood, D R; Wyatt, T R; Xie, Y; Xu, C; Yacoob, S; Yamada, R; Yang, W-C; Yasuda, T; Yatsunenko, Y A; Ye, Z; Yin, H; Yip, K; Yoo, H D; Youn, S W; Yu, J; Zeitnitz, C; Zelitch, S; Zhao, T; Zhou, B; Zhu, J; Zielinski, M; Zieminska, D; Zivkovic, L; Zutshi, V; Zverev, E G

2009-03-06

Anomalous Wtb couplings modify the angular correlations of the top-quark decay products and change the single top-quark production cross section. We present limits on anomalous top-quark couplings by combining information from W boson helicity measurements in top-quark decays and anomalous coupling searches in the single top-quark final state. We set limits on right-handed vector couplings as well as left-handed and right-handed tensor couplings based on about 1 fb(-1) of data collected by the D0 experiment.

Current Searching Methodology and Retrieval Issues: An Assessment

DTIC Science & Technology

2008-03-01

searching that are used by search engines are discussed. They are: full text searching, i.e., the searching of unstructured data, and metadata searching...also found among search engines ; however, it is the popularity of full text searching that has changed the road map to information access. The...other hand, information seekers’ willingness, or lack of, to learn the multiple search engines ’ capabilities may diminish their search results

A searching and reporting system for relational databases using a graph-based metadata representation.

PubMed

Hewitt, Robin; Gobbi, Alberto; Lee, Man-Ling

2005-01-01

Relational databases are the current standard for storing and retrieving data in the pharmaceutical and biotech industries. However, retrieving data from a relational database requires specialized knowledge of the database schema and of the SQL query language. At Anadys, we have developed an easy-to-use system for searching and reporting data in a relational database to support our drug discovery project teams. This system is fast and flexible and allows users to access all data without having to write SQL queries. This paper presents the hierarchical, graph-based metadata representation and SQL-construction methods that, together, are the basis of this system's capabilities.

Chemical Kinetics Database

National Institute of Standards and Technology Data Gateway

SRD 17 NIST Chemical Kinetics Database (Web, free access)   The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000.

Demystifying the Search Button

PubMed Central

McKeever, Liam; Nguyen, Van; Peterson, Sarah J.; Gomez-Perez, Sandra

2015-01-01

A thorough review of the literature is the basis of all research and evidence-based practice. A gold-standard efficient and exhaustive search strategy is needed to ensure all relevant citations have been captured and that the search performed is reproducible. The PubMed database comprises both the MEDLINE and non-MEDLINE databases. MEDLINE-based search strategies are robust but capture only 89% of the total available citations in PubMed. The remaining 11% include the most recent and possibly relevant citations but are only searchable through less efficient techniques. An effective search strategy must employ both the MEDLINE and the non-MEDLINE portion of PubMed to ensure all studies have been identified. The robust MEDLINE search strategies are used for the MEDLINE portion of the search. Usage of the less robust strategies is then efficiently confined to search only the remaining 11% of PubMed citations that have not been indexed for MEDLINE. The current article offers step-by-step instructions for building such a search exploring methods for the discovery of medical subject heading (MeSH) terms to search MEDLINE, text-based methods for exploring the non-MEDLINE database, information on the limitations of convenience algorithms such as the “related citations feature,” the strengths and pitfalls associated with commonly used filters, the proper usage of Boolean operators to organize a master search strategy, and instructions for automating that search through “MyNCBI” to receive search query updates by email as new citations become available. PMID:26129895

Developing Visualization Support System for Teaching/Learning Database Normalization

ERIC Educational Resources Information Center

Folorunso, Olusegun; Akinwale, AdioTaofeek

2010-01-01

Purpose: In tertiary institution, some students find it hard to learn database design theory, in particular, database normalization. The purpose of this paper is to develop a visualization tool to give students an interactive hands-on experience in database normalization process. Design/methodology/approach: The model-view-controller architecture…

Vocabulary Control and the Humanities: A Case Study of the "MLA International Bibliography."

ERIC Educational Resources Information Center

Stebelman, Scott

1994-01-01

Discussion of research in the humanities focuses on the "MLA International Bibliography," the primary database for literary research. Highlights include comparisons to research in the sciences; humanities vocabulary; database search techniques; contextual indexing; examples of searches; thesauri; and software. (43 references) (LRW)

More Databases Searched by a Business Generalist--Part 2: A Veritable Cornucopia of Sources.

ERIC Educational Resources Information Center

Meredith, Meri

1986-01-01

This second installment describes databases irregularly searched in the Business Information Center, Cummins Engine Company (Columbus, Indiana). Highlights include typical research topics (happenings among similar manufacturers); government topics (Department of Defense contracts); market and industry topics; corporate intelligence; and personnel,…